STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore

To access files for individual sequences use the datastore index:
/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log



--Next Contig--




--Next Contig--




--Next Contig--

examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log



--Next Contig--

examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log



--Next Contig--




--Next Contig--




--Next Contig--




--Next Contig--

examining contents of the fasta file and run log
examining contents of the fasta file and run log



--Next Contig--




--Next Contig--




--Next Contig--




--Next Contig--




--Next Contig--




--Next Contig--

examining contents of the fasta file and run log



--Next Contig--




--Next Contig--




--Next Contig--




--Next Contig--

examining contents of the fasta file and run log



--Next Contig--




--Next Contig--

examining contents of the fasta file and run log
examining contents of the fasta file and run log
examining contents of the fasta file and run log



--Next Contig--

examining contents of the fasta file and run log



--Next Contig--

examining contents of the fasta file and run log



--Next Contig--

examining contents of the fasta file and run log



--Next Contig--

examining contents of the fasta file and run log



--Next Contig--

examining contents of the fasta file and run log
examining contents of the fasta file and run log



--Next Contig--




--Next Contig--

examining contents of the fasta file and run log



--Next Contig--




--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283464
Length: 2096562
#---------------------------------------------------------------------





--Next Contig--

examining contents of the fasta file and run log



--Next Contig--

examining contents of the fasta file and run log
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283486
Length: 5136251
#---------------------------------------------------------------------





--Next Contig--

examining contents of the fasta file and run log
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283538
Length: 4589457
#---------------------------------------------------------------------


examining contents of the fasta file and run log
examining contents of the fasta file and run log



--Next Contig--

setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283431
Length: 1994731
#---------------------------------------------------------------------





--Next Contig--

examining contents of the fasta file and run log
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283335
Length: 1713422
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283696
Length: 1734143
#---------------------------------------------------------------------


examining contents of the fasta file and run log



--Next Contig--




--Next Contig--

examining contents of the fasta file and run log



--Next Contig--

examining contents of the fasta file and run log
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283372
Length: 1236093
#---------------------------------------------------------------------





--Next Contig--

setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283613
Length: 1538359
#---------------------------------------------------------------------





--Next Contig--




--Next Contig--




--Next Contig--

setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283650
Length: 1466308
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283556
Length: 2503893
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283579
Length: 4171015
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283560
Length: 1411826
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283543
Length: 3231396
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283657
Length: 2217704
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283707
Length: 1739591
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283672
Length: 1567882
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283508
Length: 1574934
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283713
Length: 3989156
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283547
Length: 1295974
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283724
Length: 1629761
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283748
Length: 1761904
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283790
Length: 2290191
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283765
Length: 2799266
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283832
Length: 1886876
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283859
Length: 1249076
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283853
Length: 3479538
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283742
Length: 1854155
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283898
Length: 1315257
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283899
Length: 1875070
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283885
Length: 1270075
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283918
Length: 2734180
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283926
Length: 4982860
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283957
Length: 1556749
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283903
Length: 1347673
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283991
Length: 1469071
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283967
Length: 1434804
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284013
Length: 1750930
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284025
Length: 3838175
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284039
Length: 1838760
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2283980
Length: 1571603
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284030
Length: 1661246
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284057
Length: 3576705
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284041
Length: 3474544
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
doing repeat masking
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
running  repeat masker.
doing repeat masking
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/7/blastprep/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/30/blastprep/te_proteins%2Efasta.mpi.10.1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/7/blastprep/te_proteins%2Efasta.mpi.10.2
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/7/blastprep/te_proteins%2Efasta.mpi.10.3
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/15/blastprep/te_proteins%2Efasta.mpi.10.4
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/7/blastprep/te_proteins%2Efasta.mpi.10.5
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/11/blastprep/te_proteins%2Efasta.mpi.10.6
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/11/blastprep/te_proteins%2Efasta.mpi.10.7
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/6/blastprep/te_proteins%2Efasta.mpi.10.8
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
doing blastx repeats
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
deleted:0 hits
doing blastx repeats
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/6/blastprep/te_proteins%2Efasta.mpi.10.9
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
deleted:0 hits
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
processing all repeats
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
processing all repeats
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
deleted:0 hits
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
doing blastx repeats
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
collecting blastx repeatmasking
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
doing blastx repeats
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
processing all repeats
in cluster::shadow_cluster...
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
collecting blastx repeatmasking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:1 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing repeat masking
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
doing repeat masking
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
processing all repeats
in cluster::shadow_cluster...
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
doing repeat masking
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:31   current j:0
 j_size:31   current j:1
 j_size:31   current j:2
 j_size:31   current j:3
 j_size:31   current j:4
 j_size:31   current j:5
 j_size:31   current j:6
 j_size:31   current j:7
 j_size:31   current j:8
 j_size:31   current j:9
 j_size:31   current j:10
 j_size:31   current j:11
 j_size:31   current j:12
 j_size:31   current j:13
 j_size:31   current j:14
 j_size:31   current j:15
 j_size:31   current j:16
 j_size:31   current j:17
 j_size:31   current j:18
 j_size:31   current j:19
 j_size:31   current j:20
 j_size:31   current j:21
 j_size:31   current j:22
 j_size:31   current j:23
 j_size:31   current j:24
 j_size:31   current j:25
 j_size:31   current j:26
 j_size:31   current j:27
 j_size:31   current j:28
 j_size:31   current j:29
 j_size:31   current j:30
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
processing all repeats
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:30   current j:0
 j_size:30   current j:1
 j_size:30   current j:2
 j_size:30   current j:3
 j_size:30   current j:4
 j_size:30   current j:5
 j_size:30   current j:6
 j_size:30   current j:7
 j_size:30   current j:8
 j_size:30   current j:9
 j_size:30   current j:10
 j_size:30   current j:11
 j_size:30   current j:12
 j_size:30   current j:13
 j_size:30   current j:14
 j_size:30   current j:15
 j_size:30   current j:16
 j_size:30   current j:17
 j_size:30   current j:18
 j_size:30   current j:19
 j_size:30   current j:20
 j_size:30   current j:21
 j_size:30   current j:22
 j_size:30   current j:23
 j_size:30   current j:24
 j_size:30   current j:25
 j_size:30   current j:26
 j_size:30   current j:27
 j_size:30   current j:28
 j_size:30   current j:29
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:1 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
collecting blastx repeatmasking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
collecting blastx repeatmasking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
deleted:0 hits
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
processing all repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:3 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284039.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/36/2283853.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/0/2283967.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0 -pa 1
#-------------------------------#
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284057.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/0/2283650.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/0/2283335.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/0/2283957.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2283724.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
doing repeat masking
doing blastx repeats
in cluster::shadow_cluster...
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284030.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2283724.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284039.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/36/2283853.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2283547.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284039.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2283547.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/36/2283853.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284039.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2283724.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2283547.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/36/2283853.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284039.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2283724.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2283547.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284041.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2283560.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/36/2283853.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2283967.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2283547.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2283560.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/36/2283853.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2283724.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284039.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2283967.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2283547.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284041.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2283560.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2283335.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2283903.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284039.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284041.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2283903.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2283335.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2283560.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/36/2283853.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2283650.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2283724.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284039.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2283967.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2283547.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284041.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2283335.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2283903.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2283560.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284025.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/0/2284025.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2283650.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2283957.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/36/2283853.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/76/2283853//theVoid.2283853/0/2283853.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284039.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284057.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2283859.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2283335.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2283724.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2283790.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284057.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/6B/2284057//theVoid.2284057/0/2284057.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2283967.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
ERROR: Cannot localize non-existant file /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/mpi_blastdb/te_proteins%2Efasta.mpi.10/te_proteins%2Efasta.mpi.10.2
--> rank=19, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while doing blastx repeats
ERROR: Chunk failed at level:1, tier_type:1
FAILED CONTIG:2284057

doing blastx repeats
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2284057

processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx repeats
doing blastx repeats
deleted:0 hits
doing blastx repeats
deleted:0 hits
doing blastx repeats
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
deleted:0 hits
doing blastx repeats
doing blastx repeats
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2283547.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2283967.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2283859.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2283335.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2283957.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2283724.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2283713.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2283560.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2283980.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2283650.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2283903.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/2D/2284039//theVoid.2284039/0/2284039.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner: Input/output error
ERROR: Could not open '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0E/CE/2284025//theVoid.2284025/1/2284025.10.all.rb.out'
--> rank=12, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:2284025

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2284025

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not open '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4C/87/2284030//theVoid.2284030/0/2284030.9.all.rb.out'
--> rank=16, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:2284030

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x17e12d88)', 'ARRAY(0x17f4a158)', 'ARRAY(0x185298c8)', 'runlog=HASH(0x17e6ca88)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x18502348)', 'HASH(0x17e132f8)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x17f92710)', 'run', 'HASH(0x17e87970)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x17f92710)', 17) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x17cd2b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=17, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2284039

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2284039

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2284030

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2283335.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not open '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8B/A7/2283790//theVoid.2283790/0/2283790.9.all.rb.out'
--> rank=33, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:2283790

deleted:0 hits
deleted:0 hits
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283790




--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2283859.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284058
Length: 1469289
#---------------------------------------------------------------------


deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2283560.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2283903.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
setting up GFF3 output and fasta chunks
doing blastx repeats
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/13/4F/2283547//theVoid.2283547/0/2283547.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner: Input/output error
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2283967.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2283957.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2283650.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284041.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284162
Length: 1457059
#---------------------------------------------------------------------





--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284120
Length: 5461127
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2283713.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2283543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
deleted:0 hits
deleted:0 hits



--Next Contig--

ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x17c04ef8)', 'ARRAY(0x1762d938)', 'ARRAY(0x1757a950)', 'runlog=HASH(0x17c13c28)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x174ef7a8)', 'HASH(0x17c04340)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x17c23ed0)', 'run', 'HASH(0x1764a428)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x17c23ed0)', 40) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x173c5b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=40, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283547

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283547

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284220
Length: 11517212
#---------------------------------------------------------------------


collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E9/A9/2283560//theVoid.2283560/0/2283560.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner: Input/output error
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284110
Length: 1647802
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/8E/3B/2283980//theVoid.2283980/0/2283980.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2283335.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2283903.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x1508ccd8)', 'ARRAY(0x14f73238)', 'ARRAY(0x150dec98)', 'runlog=HASH(0x156a0e88)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x1505d6d0)', 'HASH(0x150dd598)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x14fb7668)', 'run', 'HASH(0x14f66a18)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x14fb7668)', 1) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x14e78ae8)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=1, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283560

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283560

examining contents of the fasta file and run log
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2283859.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2283957.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284228
Length: 2537703
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2283967.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x1fd51e78)', 'ARRAY(0x20435648)', 'ARRAY(0x1fd72450)', 'runlog=HASH(0x1fe54128)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x1fd51e90)', 'HASH(0x1fea4918)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x1fd52328)', 'run', 'HASH(0x20435e20)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x1fd52328)', 8) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x1fc17b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=8, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283980

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283980

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2283650.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2283713.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2283335.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2283903.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FF/58/2283724//theVoid.2283724/0/2283724.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/03/2283543//theVoid.2283543/0/2283543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner: Input/output error
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2283832.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2283918.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2283859.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284232
Length: 1851861
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284013.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284041.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/55/94/2283335//theVoid.2283335/1/2283335.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2283713.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x1029f3c8)', 'ARRAY(0x10259e10)', 'ARRAY(0x10194120)', 'runlog=HASH(0x100dcf40)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x10276a08)', 'HASH(0x10246548)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x10272b48)', 'run', 'HASH(0x1082cff8)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x10272b48)', 34) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0xffd3b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=34, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283543

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x12152760)', 'ARRAY(0x12075f40)', 'ARRAY(0x12030690)', 'runlog=HASH(0x12038ef0)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x12141cc0)', 'HASH(0x12199308)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x12200c50)', 'run', 'HASH(0x120d34e0)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x12200c50)', 22) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x11f40b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=22, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283724

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2283957.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#



--Next Contig--

deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283543

deleted:0 hits
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283724

deleted:3 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284243
Length: 1752148
#---------------------------------------------------------------------


doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2283650.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2283967.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x1d3bbae8)', 'ARRAY(0x1d378c18)', 'ARRAY(0x1d45c840)', 'runlog=HASH(0x1d3fe118)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x1d3fdcc8)', 'HASH(0x1d3bf798)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x1d399ab0)', 'run', 'HASH(0x1d454f10)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x1d399ab0)', 24) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x1d26ab08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=24, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283335

deleted:0 hits
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283335

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9F/46/2283918//theVoid.2283918/0/2283918.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/E8/2283832//theVoid.2283832/0/2283832.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner: Input/output error
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/E9/2283903//theVoid.2283903/0/2283903.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2283859.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284256
Length: 1567487
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
collecting blastx repeatmasking
deleted:0 hits
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/A5/2284013//theVoid.2284013/0/2284013.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner: Input/output error
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2283957.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284041.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2283713.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284260
Length: 2107106
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

doing repeat masking
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284284
Length: 2034391
#---------------------------------------------------------------------


running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
deleted:0 hits
setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x1b9059b0)', 'ARRAY(0x1ba122a0)', 'ARRAY(0x1ba0f210)', 'runlog=HASH(0x1bfd8fc0)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x1b897fa0)', 'HASH(0x1b89d558)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x1b89af38)', 'run', 'HASH(0x1b937a78)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x1b89af38)', 2) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x1b77fae8)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=2, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283918

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283918

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x14da20d0)', 'ARRAY(0x14d5ce00)', 'ARRAY(0x14d59978)', 'runlog=HASH(0x14d983e8)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x154c3568)', 'HASH(0x14e15548)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x14dfaa50)', 'run', 'HASH(0x14e39fc8)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x14dfaa50)', 35) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x14c8bb08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=35, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283832

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283832

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x98dd940)', 'ARRAY(0x98d6d38)', 'ARRAY(0x9039608)', 'runlog=HASH(0x8e5ef68)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x8e535f0)', 'HASH(0x98d46a8)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x8dbcff8)', 'run', 'HASH(0x98d2ba0)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x8dbcff8)', 43) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x8723b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=43, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283903

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283903

deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2283650.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x20222090)', 'ARRAY(0x203cf050)', 'ARRAY(0x20949078)', 'runlog=HASH(0x20955540)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x20389df8)', 'HASH(0x203284e0)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x20208bf0)', 'run', 'HASH(0x20289808)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x20208bf0)', 10) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x20114b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=10, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2284013

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2284013

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2283859.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B0/1A/2283967//theVoid.2283967/1/2283967.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2283957.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2283713.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/88/00/2284041//theVoid.2284041/0/2284041.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner: Input/output error
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
examining contents of the fasta file and run log
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2283579.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2283650.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
deleted:0 hits
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x21af6848)', 'ARRAY(0x21b1e598)', 'ARRAY(0x21af9600)', 'runlog=HASH(0x21af6c20)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x21a0c6d0)', 'HASH(0x21985348)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x21984d78)', 'run', 'HASH(0x21a6e9a0)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x21984d78)', 7) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x21897b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=7, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283967

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283967

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--




--Next Contig--




--Next Contig--




--Next Contig--

deleted:1 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284296
Length: 1241205
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284341
Length: 1780254
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284289
Length: 2360747
#---------------------------------------------------------------------


#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284298
Length: 3464115
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
setting up GFF3 output and fasta chunks
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x150cf358)', 'ARRAY(0x156e7f50)', 'ARRAY(0x14f4b1c8)', 'runlog=HASH(0x15688640)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x1512a1d0)', 'HASH(0x15684540)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x156d8700)', 'run', 'HASH(0x150ea3b8)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x156d8700)', 18) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x14e6fb08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=18, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2284041

setting up GFF3 output and fasta chunks
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2284041

doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2283765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2283859.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2283957.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/57/2283650//theVoid.2283650/1/2283650.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
examining contents of the fasta file and run log
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
examining contents of the fasta file and run log



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284347
Length: 3379538
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2283713.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284366
Length: 3214977
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/EB/2283765//theVoid.2283765/0/2283765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AA/5F/2283579//theVoid.2283579/0/2283579.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x19581618)', 'ARRAY(0x19510070)', 'ARRAY(0x19654f88)', 'runlog=HASH(0x19520918)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x19568f40)', 'HASH(0x1950d308)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x194ae158)', 'run', 'HASH(0x194684b8)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x194ae158)', 11) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x1936fb08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=11, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283650

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283650

deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/9D/54/2283957//theVoid.2283957/1/2283957.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner: Input/output error
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x13568ce8)', 'ARRAY(0x12fbeb80)', 'ARRAY(0x12f34ad8)', 'runlog=HASH(0x12e4ce28)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x135732b0)', 'HASH(0x12f05878)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x12e789f0)', 'run', 'HASH(0x12e64fd8)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x12e789f0)', 27) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x12d5db08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=27, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283765

deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283765

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x1f429850)', 'ARRAY(0x1f2f9a38)', 'ARRAY(0x1f3e57c0)', 'runlog=HASH(0x1f4cd7e0)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x1f37d3d0)', 'HASH(0x1f2c19a8)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x1f4dc488)', 'run', 'HASH(0x1f330148)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x1f4dc488)', 3) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x1f228af8)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=3, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283579

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283579

doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x729d900)', 'ARRAY(0x6b5d1b0)', 'ARRAY(0x6af0520)', 'runlog=HASH(0x6b57c60)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x6ce9518)', 'HASH(0x6c4c940)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x6b23ef8)', 'run', 'HASH(0x72a4700)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x6b23ef8)', 5) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x6a3eb08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=5, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283957

doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2283657.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283957

examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner: Input/output error
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/FB/81/2283859//theVoid.2283859/0/2283859.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner: Input/output error
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284413
Length: 2057886
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2283713.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284424
Length: 3754818
#---------------------------------------------------------------------


doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
examining contents of the fasta file and run log
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x11732190)', 'ARRAY(0x115eab28)', 'ARRAY(0x116c1260)', 'runlog=HASH(0x11619020)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x117a65c0)', 'HASH(0x116d5a18)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x11712b20)', 'run', 'HASH(0x117a3978)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x11712b20)', 37) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x1152bb08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=37, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283859

deleted:0 hits
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283859

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/57/39/2283657//theVoid.2283657/0/2283657.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner: Input/output error
deleted:0 hits
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits



--Next Contig--

deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284436
Length: 3645435
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284439
Length: 1499190
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2283538.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0x14581988)', 'ARRAY(0x1451fa30)', 'ARRAY(0x145e0ef0)', 'runlog=HASH(0x14633400)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0x145ac4e0)', 'HASH(0x146e57d0)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0x145eb390)', 'run', 'HASH(0x14715fa8)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0x145eb390)', 13) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0x14452b08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=13, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283657

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283657

deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284450
Length: 2279540
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/25/2283713//theVoid.2283713/0/2283713.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner: Input/output error
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
cat: /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/DA/3A/2283538//theVoid.2283538/0/2283538.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner: Input/output error
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284451
Length: 1731887
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0xf825d68)', 'ARRAY(0xf5e48f0)', 'ARRAY(0xf61def0)', 'runlog=HASH(0xf6ceb20)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0xf643068)', 'HASH(0xf79b7c8)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0xf7b0538)', 'run', 'HASH(0xf76d8c0)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0xf7b0538)', 21) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0xf4edb08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=21, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283713

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283713

ERROR: Could not colapse BLAST reports
 at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/GI.pm line 2413 thread 1.
	GI::combine_blast_report('FastaChunk=HASH(0xeedccf8)', 'ARRAY(0xef92690)', 'ARRAY(0xee90178)', 'runlog=HASH(0xf039df0)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 937 thread 1
	Process::MpiChunk::__ANON__() called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 415 thread 1
	eval {...} called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Error.pm line 407 thread 1
	Error::subs::try('CODE(0xef32fc8)', 'HASH(0xeeb9788)') called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 4165 thread 1
	Process::MpiChunk::_go('Process::MpiChunk=HASH(0xeeb9938)', 'run', 'HASH(0xf5cac08)', 2, 1) called at /group/bioinfo/apps/apps/MAKER-2.28b/bin/../lib/Process/MpiChunk.pm line 341 thread 1
	Process::MpiChunk::run('Process::MpiChunk=HASH(0xeeb9938)', 32) called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 1402 thread 1
	main::node_thread('/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	eval {...} called at /apps/group/bioinformatics/apps/perl-5.16.1/lib/site_perl/5.16.1/x86_64-linux-thread-multi/forks.pm line 799 thread 1
	threads::new('threads', 'CODE(0xed8cb08)', '/scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revise...') called at /apps/group/bioinformatics/apps/MAKER-2.28b/bin/maker line 886 thread 1
--> rank=32, hostname=hansen-b089.rcac.purdue.edu
ERROR: Failed while collecting blastx repeatmasking
ERROR: Chunk failed at level:2, tier_type:1
FAILED CONTIG:2283538

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:2283538

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284461
Length: 2808225
#---------------------------------------------------------------------


doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
examining contents of the fasta file and run log



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284471
Length: 1940726
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
setting up GFF3 output and fasta chunks
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:6 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:1 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:7 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
doing blastx repeats
running  blast search.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
deleted:5 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:12 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:5 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:9 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:7 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:7 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
doing blastx repeats
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:1 hits
 sorting hits in shadow cluster...
 j_size:36   current j:0
 j_size:36   current j:1
 j_size:36   current j:2
 j_size:36   current j:3
 j_size:36   current j:4
 j_size:36   current j:5
 j_size:36   current j:6
 j_size:36   current j:7
 j_size:36   current j:8
 j_size:36   current j:9
 j_size:36   current j:10
 j_size:36   current j:11
 j_size:36   current j:12
 j_size:36   current j:13
 j_size:36   current j:14
 j_size:36   current j:15
 j_size:36   current j:16
 j_size:36   current j:17
 j_size:36   current j:18
 j_size:36   current j:19
 j_size:36   current j:20
 j_size:36   current j:21
 j_size:36   current j:22
 j_size:36   current j:23
 j_size:36   current j:24
 j_size:36   current j:25
 j_size:36   current j:26
 j_size:36   current j:27
 j_size:36   current j:28
 j_size:36   current j:29
 j_size:36   current j:30
 j_size:36   current j:31
 j_size:36   current j:32
 j_size:36   current j:33
 j_size:36   current j:34
 j_size:36   current j:35
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1 -pa 1
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
deleted:0 hits
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
processing all repeats
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx repeats
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:32   current j:0
 j_size:32   current j:1
 j_size:32   current j:2
 j_size:32   current j:3
 j_size:32   current j:4
 j_size:32   current j:5
 j_size:32   current j:6
 j_size:32   current j:7
 j_size:32   current j:8
 j_size:32   current j:9
 j_size:32   current j:10
 j_size:32   current j:11
 j_size:32   current j:12
 j_size:32   current j:13
 j_size:32   current j:14
 j_size:32   current j:15
 j_size:32   current j:16
 j_size:32   current j:17
 j_size:32   current j:18
 j_size:32   current j:19
 j_size:32   current j:20
 j_size:32   current j:21
 j_size:32   current j:22
 j_size:32   current j:23
 j_size:32   current j:24
 j_size:32   current j:25
 j_size:32   current j:26
 j_size:32   current j:27
 j_size:32   current j:28
 j_size:32   current j:29
 j_size:32   current j:30
 j_size:32   current j:31
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.0
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:30   current j:0
 j_size:30   current j:1
 j_size:30   current j:2
 j_size:30   current j:3
 j_size:30   current j:4
 j_size:30   current j:5
 j_size:30   current j:6
 j_size:30   current j:7
 j_size:30   current j:8
 j_size:30   current j:9
 j_size:30   current j:10
 j_size:30   current j:11
 j_size:30   current j:12
 j_size:30   current j:13
 j_size:30   current j:14
 j_size:30   current j:15
 j_size:30   current j:16
 j_size:30   current j:17
 j_size:30   current j:18
 j_size:30   current j:19
 j_size:30   current j:20
 j_size:30   current j:21
 j_size:30   current j:22
 j_size:30   current j:23
 j_size:30   current j:24
 j_size:30   current j:25
 j_size:30   current j:26
 j_size:30   current j:27
 j_size:30   current j:28
 j_size:30   current j:29
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.2
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx repeats
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.3
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.4
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.5
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.6
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.7
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.8
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/38/blastprep/avianuniprot%2Efasta.mpi.10.9
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
deleted:6 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
processing all repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:38   current j:0
 j_size:38   current j:1
 j_size:38   current j:2
 j_size:38   current j:3
 j_size:38   current j:4
 j_size:38   current j:5
 j_size:38   current j:6
 j_size:38   current j:7
 j_size:38   current j:8
 j_size:38   current j:9
 j_size:38   current j:10
 j_size:38   current j:11
 j_size:38   current j:12
 j_size:38   current j:13
 j_size:38   current j:14
 j_size:38   current j:15
 j_size:38   current j:16
 j_size:38   current j:17
 j_size:38   current j:18
 j_size:38   current j:19
 j_size:38   current j:20
 j_size:38   current j:21
 j_size:38   current j:22
 j_size:38   current j:23
 j_size:38   current j:24
 j_size:38   current j:25
 j_size:38   current j:26
 j_size:38   current j:27
 j_size:38   current j:28
 j_size:38   current j:29
 j_size:38   current j:30
 j_size:38   current j:31
 j_size:38   current j:32
 j_size:38   current j:33
 j_size:38   current j:34
 j_size:38   current j:35
 j_size:38   current j:36
 j_size:38   current j:37
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:4 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing masked sequence
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
processing all repeats
in cluster::shadow_cluster...
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
 sorting hits in shadow cluster...
 j_size:42   current j:0
 j_size:42   current j:1
 j_size:42   current j:2
 j_size:42   current j:3
 j_size:42   current j:4
 j_size:42   current j:5
 j_size:42   current j:6
 j_size:42   current j:7
 j_size:42   current j:8
 j_size:42   current j:9
 j_size:42   current j:10
 j_size:42   current j:11
 j_size:42   current j:12
 j_size:42   current j:13
 j_size:42   current j:14
 j_size:42   current j:15
 j_size:42   current j:16
 j_size:42   current j:17
 j_size:42   current j:18
 j_size:42   current j:19
 j_size:42   current j:20
 j_size:42   current j:21
 j_size:42   current j:22
 j_size:42   current j:23
 j_size:42   current j:24
 j_size:42   current j:25
 j_size:42   current j:26
 j_size:42   current j:27
 j_size:42   current j:28
 j_size:42   current j:29
 j_size:42   current j:30
 j_size:42   current j:31
 j_size:42   current j:32
 j_size:42   current j:33
 j_size:42   current j:34
 j_size:42   current j:35
 j_size:42   current j:36
 j_size:42   current j:37
 j_size:42   current j:38
 j_size:42   current j:39
 j_size:42   current j:40
 j_size:42   current j:41
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
collecting blastx repeatmasking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:33   current j:0
 j_size:33   current j:1
 j_size:33   current j:2
 j_size:33   current j:3
 j_size:33   current j:4
 j_size:33   current j:5
 j_size:33   current j:6
 j_size:33   current j:7
 j_size:33   current j:8
 j_size:33   current j:9
 j_size:33   current j:10
 j_size:33   current j:11
 j_size:33   current j:12
 j_size:33   current j:13
 j_size:33   current j:14
 j_size:33   current j:15
 j_size:33   current j:16
 j_size:33   current j:17
 j_size:33   current j:18
 j_size:33   current j:19
 j_size:33   current j:20
 j_size:33   current j:21
 j_size:33   current j:22
 j_size:33   current j:23
 j_size:33   current j:24
 j_size:33   current j:25
 j_size:33   current j:26
 j_size:33   current j:27
 j_size:33   current j:28
 j_size:33   current j:29
 j_size:33   current j:30
 j_size:33   current j:31
 j_size:33   current j:32
...finished clustering.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing masked sequence
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:5 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing repeat masking
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
polishing proteins
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ5ZM45%7CUBP48_CHICK.for.5769-39439.25.fasta -t /tmp/maker_6B3o0i/25/2283372.5769-39439.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.5769-39439.sp%7CQ5ZM45%7CUBP48_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning blastx...
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/6/sp%7CP55167%7CMSHR_CHICK.for.15669-17362.6.fasta -t /tmp/maker_6B3o0i/6/2283613.15669-17362.6.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/6/2283613.15669-17362.sp%7CP55167%7CMSHR_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/6/sp%7CP55167%7CMSHR_CHICK.for.80692-82430.6.fasta -t /tmp/maker_6B3o0i/6/2283613.80692-82430.6.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/6/2283613.80692-82430.sp%7CP55167%7CMSHR_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
cleaning blastx...
deleted:0 hits
deleted:0 hits
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx reports
merging blast reports...
merging blast reports...
prepare section files
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing ab-inits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
collecting blastx repeatmasking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
re-running blast for edge cases...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/25/blastprep/db.186529-213464.for_blastx.fasta
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
prepare section files
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.186529-213464.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.186529.213464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.186529.213464.0.db%2E186529-213464%2Efor_blastx%2Efasta.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing repeat masking
running  blast search.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
...finished
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:29   current j:0
 j_size:29   current j:1
 j_size:29   current j:2
 j_size:29   current j:3
 j_size:29   current j:4
 j_size:29   current j:5
 j_size:29   current j:6
 j_size:29   current j:7
 j_size:29   current j:8
 j_size:29   current j:9
 j_size:29   current j:10
 j_size:29   current j:11
 j_size:29   current j:12
 j_size:29   current j:13
 j_size:29   current j:14
 j_size:29   current j:15
 j_size:29   current j:16
 j_size:29   current j:17
 j_size:29   current j:18
 j_size:29   current j:19
 j_size:29   current j:20
 j_size:29   current j:21
 j_size:29   current j:22
 j_size:29   current j:23
 j_size:29   current j:24
 j_size:29   current j:25
 j_size:29   current j:26
 j_size:29   current j:27
 j_size:29   current j:28
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
polishing proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28568%7CGTR3_CHICK.for.200205-203864.25.fasta -t /tmp/maker_6B3o0i/25/2283372.200205-203864.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.200205-203864.sp%7CP28568%7CGTR3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ90592%7CGTR2_CHICK.for.200247-203798.25.fasta -t /tmp/maker_6B3o0i/25/2283372.200247-203798.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.200247-203798.sp%7CQ90592%7CGTR2_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP46896%7CGTR1_CHICK.for.196129-203864.25.fasta -t /tmp/maker_6B3o0i/25/2283372.196129-203864.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.196129-203864.sp%7CP46896%7CGTR1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
collecting blastx repeatmasking
in cluster::shadow_cluster...
doing blastx repeats
collecting blastx repeatmasking
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ5ZKJ4%7CFGOP2_CHICK.for.53664-61618.9.fasta -t /tmp/maker_6B3o0i/9/2283991.53664-61618.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.53664-61618.sp%7CQ5ZKJ4%7CFGOP2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx repeatmasking
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ06066%7CYBOX1_CHICK.for.302774-311039.25.fasta -t /tmp/maker_6B3o0i/25/2283372.302774-311039.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.302774-311039.sp%7CQ06066%7CYBOX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ6JHU8%7CP3H1_CHICK.for.330364-341212.25.fasta -t /tmp/maker_6B3o0i/25/2283372.330364-341212.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.330364-341212.sp%7CQ6JHU8%7CP3H1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ6JHU7%7CP3H2_CHICK.for.330572-337627.25.fasta -t /tmp/maker_6B3o0i/25/2283372.330572-337627.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.330572-337627.sp%7CQ6JHU7%7CP3H2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ9PSX7%7CRHOC_CHICK.for.380488-381787.25.fasta -t /tmp/maker_6B3o0i/25/2283372.380488-381787.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.380488-381787.sp%7CQ9PSX7%7CRHOC_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ90694%7CCDC42_CHICK.for.373174-387686.25.fasta -t /tmp/maker_6B3o0i/25/2283372.373174-387686.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.373174-387686.sp%7CQ90694%7CCDC42_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx reports
merging blast reports...
merging blast reports...
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing ab-inits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
doing blastx repeats
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
collecting blastx repeatmasking
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:33   current j:0
 j_size:33   current j:1
 j_size:33   current j:2
 j_size:33   current j:3
 j_size:33   current j:4
 j_size:33   current j:5
 j_size:33   current j:6
 j_size:33   current j:7
 j_size:33   current j:8
 j_size:33   current j:9
 j_size:33   current j:10
 j_size:33   current j:11
 j_size:33   current j:12
 j_size:33   current j:13
 j_size:33   current j:14
 j_size:33   current j:15
 j_size:33   current j:16
 j_size:33   current j:17
 j_size:33   current j:18
 j_size:33   current j:19
 j_size:33   current j:20
 j_size:33   current j:21
 j_size:33   current j:22
 j_size:33   current j:23
 j_size:33   current j:24
 j_size:33   current j:25
 j_size:33   current j:26
 j_size:33   current j:27
 j_size:33   current j:28
 j_size:33   current j:29
 j_size:33   current j:30
 j_size:33   current j:31
 j_size:33   current j:32
...finished clustering.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/0/2283885.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
preparing ab-inits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
prepare section files
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28127%7CWNT4_MELGA.for.417950-419106.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417950-419106.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417950-419106.sp%7CP28127%7CWNT4_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28128%7CWNT5A_MELGA.for.417950-419106.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417950-419106.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417950-419106.sp%7CP28128%7CWNT5A_MELGA.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28129%7CWNT7A_MELGA.for.417950-419106.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417950-419106.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417950-419106.sp%7CP28129%7CWNT7A_MELGA.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP49339%7CWNT11_CHICK.for.417887-422412.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417887-422412.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417887-422412.sp%7CP49339%7CWNT11_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ3L254%7CWNT7B_CHICK.for.417887-422412.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417887-422412.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417887-422412.sp%7CQ3L254%7CWNT7B_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ91029%7CWNT1_CHICK.for.417917-422358.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417917-422358.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417917-422358.sp%7CQ91029%7CWNT1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28130%7CWNT7B_MELGA.for.417950-419106.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417950-419106.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417950-419106.sp%7CP28130%7CWNT7B_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ98SN7%7CWNT2B_CHICK.for.417887-422394.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417887-422394.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417887-422394.sp%7CQ98SN7%7CWNT2B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP51030%7CWNT8C_CHICK.for.417890-420004.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417890-420004.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417890-420004.sp%7CP51030%7CWNT8C_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ2LMP1%7CWNT3A_CHICK.for.417887-422367.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417887-422367.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417887-422367.sp%7CQ2LMP1%7CWNT3A_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28125%7CWNT3A_MELGA.for.417950-419106.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417950-419106.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417950-419106.sp%7CP28125%7CWNT3A_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28126%7CWNT3B_MELGA.for.417950-419106.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417950-419106.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417950-419106.sp%7CP28126%7CWNT3B_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP49337%7CWNT4_CHICK.for.417887-422415.25.fasta -t /tmp/maker_6B3o0i/25/2283372.417887-422415.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.417887-422415.sp%7CP49337%7CWNT4_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 13
 ...processing 1 of 13
 ...processing 2 of 13
 ...processing 3 of 13
 ...processing 4 of 13
 ...processing 5 of 13
 ...processing 6 of 13
 ...processing 7 of 13
 ...processing 8 of 13
 ...processing 9 of 13
 ...processing 10 of 13
deleted:0 hits
 ...processing 11 of 13
 ...processing 12 of 13
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 11
 ...processing 1 of 11
 ...processing 2 of 11
 ...processing 3 of 11
 ...processing 4 of 11
 ...processing 5 of 11
 ...processing 6 of 11
 ...processing 7 of 11
 ...processing 8 of 11
 ...processing 9 of 11
 ...processing 10 of 11
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
collecting blastx reports
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
doing repeat masking
processing all repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
collecting blastx repeatmasking
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
deleted:0 hits
collecting blastx reports
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/38/sp%7CP18943%7CCOX1_CHICK.for.1029231-1031471.38.fasta -t /tmp/maker_6B3o0i/38/2283885.1029231-1031471.38.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/38/2283885.1029231-1031471.sp%7CP18943%7CCOX1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/38/sp%7CP18937%7CNU2M_CHICK.for.1031111-1032859.38.fasta -t /tmp/maker_6B3o0i/38/2283885.1031111-1032859.38.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/38/2283885.1031111-1032859.sp%7CP18937%7CNU2M_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/38/sp%7CP18936%7CNU1M_CHICK.for.1032287-1033983.38.fasta -t /tmp/maker_6B3o0i/38/2283885.1032287-1033983.38.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/38/2283885.1032287-1033983.sp%7CP18936%7CNU1M_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:31   current j:0
 j_size:31   current j:1
 j_size:31   current j:2
 j_size:31   current j:3
 j_size:31   current j:4
 j_size:31   current j:5
 j_size:31   current j:6
 j_size:31   current j:7
 j_size:31   current j:8
 j_size:31   current j:9
 j_size:31   current j:10
 j_size:31   current j:11
 j_size:31   current j:12
 j_size:31   current j:13
 j_size:31   current j:14
 j_size:31   current j:15
 j_size:31   current j:16
 j_size:31   current j:17
 j_size:31   current j:18
 j_size:31   current j:19
 j_size:31   current j:20
 j_size:31   current j:21
 j_size:31   current j:22
 j_size:31   current j:23
 j_size:31   current j:24
 j_size:31   current j:25
 j_size:31   current j:26
 j_size:31   current j:27
 j_size:31   current j:28
 j_size:31   current j:29
 j_size:31   current j:30
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
prepare section files
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2283885.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D5/C1/2283885//theVoid.2283885/1/2283885.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:5 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:32   current j:0
 j_size:32   current j:1
 j_size:32   current j:2
 j_size:32   current j:3
 j_size:32   current j:4
 j_size:32   current j:5
 j_size:32   current j:6
 j_size:32   current j:7
 j_size:32   current j:8
 j_size:32   current j:9
 j_size:32   current j:10
 j_size:32   current j:11
 j_size:32   current j:12
 j_size:32   current j:13
 j_size:32   current j:14
 j_size:32   current j:15
 j_size:32   current j:16
 j_size:32   current j:17
 j_size:32   current j:18
 j_size:32   current j:19
 j_size:32   current j:20
 j_size:32   current j:21
 j_size:32   current j:22
 j_size:32   current j:23
 j_size:32   current j:24
 j_size:32   current j:25
 j_size:32   current j:26
 j_size:32   current j:27
 j_size:32   current j:28
 j_size:32   current j:29
 j_size:32   current j:30
 j_size:32   current j:31
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing the chunk divide
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CO42409%7CGFI1B_CHICK.for.634947-637721.25.fasta -t /tmp/maker_6B3o0i/25/2283372.634947-637721.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.634947-637721.sp%7CO42409%7CGFI1B_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ92010%7CZBT14_CHICK.for.634959-637064.25.fasta -t /tmp/maker_6B3o0i/25/2283372.634959-637064.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.634959-637064.sp%7CQ92010%7CZBT14_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CO73693%7CEGR1_TAEGU.for.636051-637070.25.fasta -t /tmp/maker_6B3o0i/25/2283372.636051-637070.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.636051-637070.sp%7CO73693%7CEGR1_TAEGU.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
deleted:0 hits
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx repeats
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:2 hits
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
deleted:1 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:1 hits
prepare section files
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/0/2283898.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:5 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP49285%7CMTR1A_CHICK.for.234170-235839.15.fasta -t /tmp/maker_6B3o0i/15/2283696.234170-235839.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2283696.234170-235839.sp%7CP49285%7CMTR1A_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP51050%7CMTR1B_CHICK.for.234170-235836.15.fasta -t /tmp/maker_6B3o0i/15/2283696.234170-235836.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2283696.234170-235836.sp%7CP51050%7CMTR1B_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP49288%7CMTR1C_CHICK.for.234179-235839.15.fasta -t /tmp/maker_6B3o0i/15/2283696.234179-235839.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2283696.234179-235839.sp%7CP49288%7CMTR1C_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
flattening protein clusters
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:2 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
merging blast reports...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28693%7CEPHB2_CHICK.for.728699-740741.25.fasta -t /tmp/maker_6B3o0i/25/2283372.728699-740741.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.728699-740741.sp%7CP28693%7CEPHB2_CHICK.p.exonerate
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ07498%7CEPHB3_CHICK.for.728699-740771.25.fasta -t /tmp/maker_6B3o0i/25/2283372.728699-740771.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.728699-740771.sp%7CQ07498%7CEPHB3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ07497%7CEPHB5_CHICK.for.728624-740744.25.fasta -t /tmp/maker_6B3o0i/25/2283372.728624-740744.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.728624-740744.sp%7CQ07497%7CEPHB5_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ02977%7CYRK_CHICK.for.735803-740702.25.fasta -t /tmp/maker_6B3o0i/25/2283372.735803-740702.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.735803-740702.sp%7CQ02977%7CYRK_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP29318%7CEPHA3_CHICK.for.727465-740732.25.fasta -t /tmp/maker_6B3o0i/25/2283372.727465-740732.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.727465-740732.sp%7CP29318%7CEPHA3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ07496%7CEPHA4_CHICK.for.727465-740744.25.fasta -t /tmp/maker_6B3o0i/25/2283372.727465-740744.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.727465-740744.sp%7CQ07496%7CEPHA4_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP00523%7CSRC_CHICK.for.735818-740702.25.fasta -t /tmp/maker_6B3o0i/25/2283372.735818-740702.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.735818-740702.sp%7CP00523%7CSRC_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP54755%7CEPHA5_CHICK.for.727465-740732.25.fasta -t /tmp/maker_6B3o0i/25/2283372.727465-740732.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.727465-740732.sp%7CP54755%7CEPHA5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CO42422%7CEPHA7_CHICK.for.727468-740732.25.fasta -t /tmp/maker_6B3o0i/25/2283372.727468-740732.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.727468-740732.sp%7CO42422%7CEPHA7_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ07494%7CEPHB1_CHICK.for.727465-741311.25.fasta -t /tmp/maker_6B3o0i/25/2283372.727465-741311.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.727465-741311.sp%7CQ07494%7CEPHB1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP09324%7CYES_CHICK.for.735791-740702.25.fasta -t /tmp/maker_6B3o0i/25/2283372.735791-740702.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.735791-740702.sp%7CP09324%7CYES_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ05876%7CFYN_CHICK.for.735827-740702.25.fasta -t /tmp/maker_6B3o0i/25/2283372.735827-740702.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.735827-740702.sp%7CQ05876%7CFYN_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
collecting blastx reports
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx repeats
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
gathering ab-init output files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:-2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:-1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:1 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:-1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-2 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
prepare section files
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
re-running blast for edge cases...
doing blastx repeats
running  blast search.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/15/blastprep/db.385169-419208.for_blastx.fasta
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.385169-419208.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.385169.419208.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.385169.419208.0.db%2E385169-419208%2Efor_blastx%2Efasta.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:12 hits
...finished
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
deleted:2 hits
doing blastx of proteins
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ9PU53%7CTERF2_CHICK.for.18587-28476.20.fasta -t /tmp/maker_6B3o0i/20/2283707.18587-28476.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2283707.18587-28476.sp%7CQ9PU53%7CTERF2_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP08641%7CCADH1_CHICK.for.459513-460696.15.fasta -t /tmp/maker_6B3o0i/15/2283696.459513-460696.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2283696.459513-460696.sp%7CP08641%7CCADH1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CP00174%7CCYB5_CHICK.for.47028-47959.20.fasta -t /tmp/maker_6B3o0i/20/2283707.47028-47959.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2283707.47028-47959.sp%7CP00174%7CCYB5_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
running  blast search.
flattening protein clusters
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing masked sequence
deleted:2 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:29   current j:0
 j_size:29   current j:1
 j_size:29   current j:2
 j_size:29   current j:3
 j_size:29   current j:4
 j_size:29   current j:5
 j_size:29   current j:6
 j_size:29   current j:7
 j_size:29   current j:8
 j_size:29   current j:9
 j_size:29   current j:10
 j_size:29   current j:11
 j_size:29   current j:12
 j_size:29   current j:13
 j_size:29   current j:14
 j_size:29   current j:15
 j_size:29   current j:16
 j_size:29   current j:17
 j_size:29   current j:18
 j_size:29   current j:19
 j_size:29   current j:20
 j_size:29   current j:21
 j_size:29   current j:22
 j_size:29   current j:23
 j_size:29   current j:24
 j_size:29   current j:25
 j_size:29   current j:26
 j_size:29   current j:27
 j_size:29   current j:28
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
gathering ab-init output files
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/0/2283372.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
deleted:0 hits
Making transcripts
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/0/2283613.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP28693%7CEPHB2_CHICK.for.957900-983242.25.fasta -t /tmp/maker_6B3o0i/25/2283372.957900-983242.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.957900-983242.sp%7CP28693%7CEPHB2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ07498%7CEPHB3_CHICK.for.957864-983242.25.fasta -t /tmp/maker_6B3o0i/25/2283372.957864-983242.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.957864-983242.sp%7CQ07498%7CEPHB3_CHICK.p.exonerate
#-------------------------------#
collecting blastx reports
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ07497%7CEPHB5_CHICK.for.957903-983242.25.fasta -t /tmp/maker_6B3o0i/25/2283372.957903-983242.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.957903-983242.sp%7CQ07497%7CEPHB5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ07494%7CEPHB1_CHICK.for.957900-983224.25.fasta -t /tmp/maker_6B3o0i/25/2283372.957900-983224.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2283372.957900-983224.sp%7CQ07494%7CEPHB1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CQ5F3G7%7CC1GLT_CHICK.for.568881-574656.14.fasta -t /tmp/maker_6B3o0i/14/2283672.568881-574656.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2283672.568881-574656.sp%7CQ5F3G7%7CC1GLT_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
cleaning blastx...
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/0/2283508.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2283898.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/35/74/2283898//theVoid.2283898/1/2283898.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CQ9DED6%7CBAX1B_CHICK.for.1226575-1227935.39.fasta -t /tmp/maker_6B3o0i/39/2283898.1226575-1227935.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2283898.1226575-1227935.sp%7CQ9DED6%7CBAX1B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CQ9W6D8%7CBARX1_CHICK.for.1226575-1227839.39.fasta -t /tmp/maker_6B3o0i/39/2283898.1226575-1227839.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2283898.1226575-1227839.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284484
Length: 1324922
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
deleted:0 hits
collecting blastx reports
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
processing the chunk divide
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:-1 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CQ5ZJU3%7CASNS_CHICK.for.608915-619607.14.fasta -t /tmp/maker_6B3o0i/14/2283672.608915-619607.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2283672.608915-619607.sp%7CQ5ZJU3%7CASNS_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CQ5ZJU3%7CASNS_CHICK.for.632620-635462.14.fasta -t /tmp/maker_6B3o0i/14/2283672.632620-635462.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2283672.632620-635462.sp%7CQ5ZJU3%7CASNS_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:29   current j:0
 j_size:29   current j:1
 j_size:29   current j:2
 j_size:29   current j:3
 j_size:29   current j:4
 j_size:29   current j:5
 j_size:29   current j:6
 j_size:29   current j:7
 j_size:29   current j:8
 j_size:29   current j:9
 j_size:29   current j:10
 j_size:29   current j:11
 j_size:29   current j:12
 j_size:29   current j:13
 j_size:29   current j:14
 j_size:29   current j:15
 j_size:29   current j:16
 j_size:29   current j:17
 j_size:29   current j:18
 j_size:29   current j:19
 j_size:29   current j:20
 j_size:29   current j:21
 j_size:29   current j:22
 j_size:29   current j:23
 j_size:29   current j:24
 j_size:29   current j:25
 j_size:29   current j:26
 j_size:29   current j:27
 j_size:29   current j:28
...finished clustering.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0 -pa 1
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0 -pa 1
#-------------------------------#
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2283372.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CE/74/2283372//theVoid.2283372/1/2283372.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/0/2283991.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing the chunk divide
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:-1 hits
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ90762%7CCADH6_CHICK.for.1122232-1136292.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1122232-1136292.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1122232-1136292.sp%7CQ90762%7CCADH6_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ90763%7CCADH7_CHICK.for.1122253-1136301.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1122253-1136301.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1122253-1136301.sp%7CQ90763%7CCADH7_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CP79995%7CCAD10_CHICK.for.1122232-1136292.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1122232-1136292.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1122232-1136292.sp%7CP79995%7CCAD10_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CO93319%7CCAD11_CHICK.for.1122241-1136280.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1122241-1136280.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1122241-1136280.sp%7CO93319%7CCAD11_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ8QGH3%7CCAD20_CHICK.for.1122241-1136292.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1122241-1136292.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1122241-1136292.sp%7CQ8QGH3%7CCAD20_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ90762%7CCADH6_CHICK.for.1147142-1154043.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1147142-1154043.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1147142-1154043.sp%7CQ90762%7CCADH6_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ90763%7CCADH7_CHICK.for.1147148-1154043.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1147148-1154043.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1147148-1154043.sp%7CQ90763%7CCADH7_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CP79995%7CCAD10_CHICK.for.1147133-1154043.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1147133-1154043.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1147133-1154043.sp%7CP79995%7CCAD10_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CO93319%7CCAD11_CHICK.for.1147139-1154043.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1147139-1154043.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1147139-1154043.sp%7CO93319%7CCAD11_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ8QGH3%7CCAD20_CHICK.for.1147142-1154043.31.fasta -t /tmp/maker_6B3o0i/31/2283508.1147142-1154043.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2283508.1147142-1154043.sp%7CQ8QGH3%7CCAD20_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
flattening protein clusters
doing blastx repeats
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/0/2284120.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
prepare section files
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0 -pa 1
#-------------------------------#
polishing proteins
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP08642%7CRASH_CHICK.for.1027210-1037081.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1027210-1037081.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1027210-1037081.sp%7CP08642%7CRASH_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP79800%7CRASK_MELGA.for.1027210-1037081.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1027210-1037081.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1027210-1037081.sp%7CP79800%7CRASK_MELGA.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ5F352%7CRASN_CHICK.for.1027210-1044531.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1027210-1044531.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1027210-1044531.sp%7CQ5F352%7CRASN_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ5ZHX1%7CRAP1B_CHICK.for.1027210-1037078.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1027210-1037078.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1027210-1037078.sp%7CQ5ZHX1%7CRAP1B_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CB5FXA0%7CLYRM5_TAEGU.for.1054676-1055730.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1054676-1055730.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1054676-1055730.sp%7CB5FXA0%7CLYRM5_TAEGU.p.exonerate
#-------------------------------#
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:2 now processing 0
deleted:1 hits
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
deleted:0 hits
collecting blastx reports
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
processing all repeats
prepare section files
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
prepare section files
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
preparing evidence clusters for annotations
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1 -pa 1
#-------------------------------#
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
re-running blast for edge cases...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/23/blastprep/db.289576-314709.for_blastx.fasta
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.289576-314709.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.289576.314709.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.289576.314709.0.db%2E289576-314709%2Efor_blastx%2Efasta.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ9DE13%7CBAZ2B_CHICK.for.319287-340637.23.fasta -t /tmp/maker_6B3o0i/23/2283742.319287-340637.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.319287-340637.sp%7CQ9DE13%7CBAZ2B_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ5ZMC3%7CWSDU1_CHICK.for.368830-383827.23.fasta -t /tmp/maker_6B3o0i/23/2283742.368830-383827.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.368830-383827.sp%7CQ5ZMC3%7CWSDU1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 12
 ...processing 1 of 12
 ...processing 2 of 12
 ...processing 3 of 12
collecting blastx repeatmasking
 ...processing 4 of 12
 ...processing 5 of 12
 ...processing 6 of 12
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 7 of 12
 ...processing 8 of 12
 ...processing 9 of 12
 ...processing 10 of 12
 ...processing 11 of 12
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/6/sp%7CQ90762%7CCADH6_CHICK.for.1319649-1351823.6.fasta -t /tmp/maker_6B3o0i/6/2283613.1319649-1351823.6.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/6/2283613.1319649-1351823.sp%7CQ90762%7CCADH6_CHICK.p.exonerate
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/6/sp%7CQ90763%7CCADH7_CHICK.for.1319649-1351844.6.fasta -t /tmp/maker_6B3o0i/6/2283613.1319649-1351844.6.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/6/2283613.1319649-1351844.sp%7CQ90763%7CCADH7_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/0/2283672.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/6/sp%7CP79995%7CCAD10_CHICK.for.1319649-1351826.6.fasta -t /tmp/maker_6B3o0i/6/2283613.1319649-1351826.6.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/6/2283613.1319649-1351826.sp%7CP79995%7CCAD10_CHICK.p.exonerate
#-------------------------------#
collecting blastx reports
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/6/sp%7CO93319%7CCAD11_CHICK.for.1319649-1351823.6.fasta -t /tmp/maker_6B3o0i/6/2283613.1319649-1351823.6.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/6/2283613.1319649-1351823.sp%7CO93319%7CCAD11_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/6/sp%7CQ8QGH3%7CCAD20_CHICK.for.1319649-1351820.6.fasta -t /tmp/maker_6B3o0i/6/2283613.1319649-1351820.6.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/6/2283613.1319649-1351820.sp%7CQ8QGH3%7CCAD20_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CP50577%7CDLX5_CHICK.for.986078-987966.14.fasta -t /tmp/maker_6B3o0i/14/2283672.986078-987966.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2283672.986078-987966.sp%7CP50577%7CDLX5_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
cleaning blastx...
preparing evidence clusters for annotations
cleaning clusters....
total clusters:1 now processing 0
Preparing evidence for hint based annotation
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
deleted:0 hits
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/0/2283696.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP70081%7CH48_CHICK.for.919590-920611.15.fasta -t /tmp/maker_6B3o0i/15/2283696.919590-920611.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2283696.919590-920611.sp%7CP70081%7CH48_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP62801%7CH4_CHICK.for.919590-920611.15.fasta -t /tmp/maker_6B3o0i/15/2283696.919590-920611.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2283696.919590-920611.sp%7CP62801%7CH4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing contig output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284485
Length: 2432434
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ5F478%7CANR44_CHICK.for.408222-409538.23.fasta -t /tmp/maker_6B3o0i/23/2283742.408222-409538.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.408222-409538.sp%7CQ5F478%7CANR44_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
doing blastx of proteins
doing blastx of proteins
 ...processing 4 of 5
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
deleted:0 hits
 ...processing 5 of 6
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2283613.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/71/40/2283613//theVoid.2283613/1/2283613.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx repeats
adding statistics to annotations
Calculating annotation quality statistics
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP00340%7CLDHA_CHICK.for.1277682-1285006.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1277682-1285006.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1277682-1285006.sp%7CP00340%7CLDHA_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ9PW07%7CLDHA_COLLI.for.1277682-1285006.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1277682-1285006.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1277682-1285006.sp%7CQ9PW07%7CLDHA_COLLI.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP00337%7CLDHB_CHICK.for.1277676-1289302.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1277676-1289302.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1277676-1289302.sp%7CP00337%7CLDHB_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ9PW04%7CLDHB_COLLI.for.1277676-1289302.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1277676-1289302.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1277676-1289302.sp%7CQ9PW04%7CLDHB_COLLI.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
deleted:0 hits
 ...processing 2 of 4
 ...processing 3 of 4
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2283508.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/53/B5/2283508//theVoid.2283508/1/2283508.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/42/sp%7CP26990%7CARF6_CHICK.for.14044-14990.42.fasta -t /tmp/maker_6B3o0i/42/2283899.14044-14990.42.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/42/2283899.14044-14990.sp%7CP26990%7CARF6_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
collecting blastx reports
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing the chunk divide
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
polishing proteins
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CQ6RFL5%7CBSH_CHICK.for.1005293-1006269.14.fasta -t /tmp/maker_6B3o0i/14/2283672.1005293-1006269.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2283672.1005293-1006269.sp%7CQ6RFL5%7CBSH_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CP50577%7CDLX5_CHICK.for.1003317-1006299.14.fasta -t /tmp/maker_6B3o0i/14/2283672.1003317-1006299.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2283672.1003317-1006299.sp%7CP50577%7CDLX5_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
merging blast reports...
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
collecting blastx reports
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing all repeats
choosing best annotation set
Choosing best annotations
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
processing the chunk divide
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
preparing evidence clusters for annotations
deleted:0 hits
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx repeats
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
collecting blastx reports
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
doing blastx repeats
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing chunk output
doing blastx of proteins
processing all repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing masked sequence
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing ab-inits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
gathering ab-init output files
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing repeat masking
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2283991.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/DB/2283991//theVoid.2283991/1/2283991.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
collecting blastx reports
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CF1NHE9%7CIRK12_CHICK.for.1376518-1382090.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1376518-1382090.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1376518-1382090.sp%7CF1NHE9%7CIRK12_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1 -pa 1
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP52186%7CIRK2_CHICK.for.1376563-1382108.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1376563-1382108.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1376563-1382108.sp%7CP52186%7CIRK2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ90854%7CIRK3_CHICK.for.1376578-1382177.9.fasta -t /tmp/maker_6B3o0i/9/2283991.1376578-1382177.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2283991.1376578-1382177.sp%7CQ90854%7CIRK3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
choosing best annotation set
Choosing best annotations
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing chunk output
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
collecting blastx reports
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing the chunk divide
processing contig output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1 -pa 1
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
running  blast search.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
collecting blastx reports
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#



--Next Contig--

deleted:0 hits
preparing masked sequence
prepare section files
deleted:0 hits
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284495
Length: 1857782
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
deleted:0 hits
deleted:0 hits
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing ab-inits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/0/2284220.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
preparing evidence clusters for annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
flattening protein clusters
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/1/2283486.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
processing chunk output
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
doing repeat masking
Preparing evidence for hint based annotation
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:1 hits
flattening protein clusters
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
collecting blastx reports
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
polishing proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ8QG61%7CCRY1_CHICK.for.80669-94586.26.fasta -t /tmp/maker_6B3o0i/26/2283748.80669-94586.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.80669-94586.sp%7CQ8QG61%7CCRY1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ8QG60%7CCRY2_CHICK.for.80666-94586.26.fasta -t /tmp/maker_6B3o0i/26/2283748.80666-94586.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.80666-94586.sp%7CQ8QG60%7CCRY2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ5ZKD1%7CCEPT1_CHICK.for.178268-184332.26.fasta -t /tmp/maker_6B3o0i/26/2283748.178268-184332.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.178268-184332.sp%7CQ5ZKD1%7CCEPT1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ5ZHQ5%7CCHPT1_CHICK.for.178391-184329.26.fasta -t /tmp/maker_6B3o0i/26/2283748.178391-184329.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.178391-184329.sp%7CQ5ZHQ5%7CCHPT1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1 -pa 1
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
choosing best annotation set
Choosing best annotations
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:-1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/0/2283707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:1 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
processing chunk output
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ5ZKD1%7CCEPT1_CHICK.for.221318-225512.26.fasta -t /tmp/maker_6B3o0i/26/2283748.221318-225512.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.221318-225512.sp%7CQ5ZKD1%7CCEPT1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ5ZHQ5%7CCHPT1_CHICK.for.221315-224580.26.fasta -t /tmp/maker_6B3o0i/26/2283748.221315-224580.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.221315-224580.sp%7CQ5ZHQ5%7CCHPT1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ05623%7CMYBPH_CHICK.for.272036-279426.26.fasta -t /tmp/maker_6B3o0i/26/2283748.272036-279426.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.272036-279426.sp%7CQ05623%7CMYBPH_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
choosing best annotation set
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP49892%7CAA1R_CHICK.for.284388-285820.26.fasta -t /tmp/maker_6B3o0i/26/2283748.284388-285820.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.284388-285820.sp%7CP49892%7CAA1R_CHICK.p.exonerate
#-------------------------------#
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
processing chunk output
running  blast search.
doing blastx of proteins
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1 -pa 1
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CO13076%7CAA2BR_CHICK.for.284394-285820.26.fasta -t /tmp/maker_6B3o0i/26/2283748.284394-285820.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.284394-285820.sp%7CO13076%7CAA2BR_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
preparing evidence clusters for annotations
running  blast search.
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
preparing evidence clusters for annotations
running  blast search.
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2283672.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/DB/2283672//theVoid.2283672/1/2283672.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing all repeats
running  blast search.
choosing best annotation set
Choosing best annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/42/sp%7CQ5ZIN0%7CABD12_CHICK.for.457607-459552.42.fasta -t /tmp/maker_6B3o0i/42/2283899.457607-459552.42.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/42/2283899.457607-459552.sp%7CQ5ZIN0%7CABD12_CHICK.p.exonerate
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
cleaning blastx...
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
merging blast reports...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
flattening protein clusters
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
collecting blastx repeatmasking
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CO73590%7CZFHX4_CHICK.for.1014576-1022711.20.fasta -t /tmp/maker_6B3o0i/20/2283707.1014576-1022711.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2283707.1014576-1022711.sp%7CO73590%7CZFHX4_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 6
 ...processing 1 of 6
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 2 of 6
processing all repeats
doing blastx repeats
 ...processing 3 of 6
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
processing the chunk divide
doing blastx of proteins
running  blast search.
 ...processing 4 of 6
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
 ...processing 5 of 6
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/0/2283742.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx reports
prepare section files
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing contig output
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
examining contents of the fasta file and run log
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
polishing proteins



--Next Contig--

running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP49892%7CAA1R_CHICK.for.309389-310551.26.fasta -t /tmp/maker_6B3o0i/26/2283748.309389-310551.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.309389-310551.sp%7CP49892%7CAA1R_CHICK.p.exonerate
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284498
Length: 1448801
#---------------------------------------------------------------------


running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CO13076%7CAA2BR_CHICK.for.309371-310539.26.fasta -t /tmp/maker_6B3o0i/26/2283748.309371-310539.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.309371-310539.sp%7CO13076%7CAA2BR_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
setting up GFF3 output and fasta chunks
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ01795%7CMYF6_CHICK.for.324541-325781.26.fasta -t /tmp/maker_6B3o0i/26/2283748.324541-325781.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.324541-325781.sp%7CQ01795%7CMYF6_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP16075%7CMYOD1_CHICK.for.324721-325796.26.fasta -t /tmp/maker_6B3o0i/26/2283748.324721-325796.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.324721-325796.sp%7CP16075%7CMYOD1_CHICK.p.exonerate
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP17920%7CMYOG_CHICK.for.324541-325799.26.fasta -t /tmp/maker_6B3o0i/26/2283748.324541-325799.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.324541-325799.sp%7CP17920%7CMYOG_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ08856%7CMYF5_CHICK.for.324541-325751.26.fasta -t /tmp/maker_6B3o0i/26/2283748.324541-325751.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.324541-325751.sp%7CQ08856%7CMYF5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1 -pa 1
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1 -pa 1
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:1 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing contig output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
processing chunk output
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:-1 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
examining contents of the fasta file and run log
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#



--Next Contig--

doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284509
Length: 3419647
#---------------------------------------------------------------------


doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CO73590%7CZFHX4_CHICK.for.1127744-1133865.20.fasta -t /tmp/maker_6B3o0i/20/2283707.1127744-1133865.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2283707.1127744-1133865.sp%7CO73590%7CZFHX4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ9PVY0%7CRX1_CHICK.for.1130381-1131351.20.fasta -t /tmp/maker_6B3o0i/20/2283707.1130381-1131351.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2283707.1130381-1131351.sp%7CQ9PVY0%7CRX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
 ...processing 0 of 3
 ...processing 1 of 3
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
 ...processing 2 of 3
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
prepare section files
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
re-running blast for edge cases...
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/23/blastprep/db.988545-1032424.for_blastx.fasta
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.988545-1032424.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.988545.1032424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.988545.1032424.0.db%2E988545-1032424%2Efor_blastx%2Efasta.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
...finished
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
running  blast search.
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ90670%7CAVR2B_CHICK.for.1007416-1011197.23.fasta -t /tmp/maker_6B3o0i/23/2283742.1007416-1011197.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.1007416-1011197.sp%7CQ90670%7CAVR2B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ90669%7CAVR2A_CHICK.for.1007416-1014917.23.fasta -t /tmp/maker_6B3o0i/23/2283742.1007416-1014917.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.1007416-1014917.sp%7CQ90669%7CAVR2A_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ05438%7CBMR1B_CHICK.for.1007416-1022806.23.fasta -t /tmp/maker_6B3o0i/23/2283742.1007416-1022806.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.1007416-1022806.sp%7CQ05438%7CBMR1B_CHICK.p.exonerate
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ90ZK6%7CACVR1_CHICK.for.998145-1022824.23.fasta -t /tmp/maker_6B3o0i/23/2283742.998145-1022824.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.998145-1022824.sp%7CQ90ZK6%7CACVR1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ90999%7CTGFR2_CHICK.for.1081356-1084022.23.fasta -t /tmp/maker_6B3o0i/23/2283742.1081356-1084022.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.1081356-1084022.sp%7CQ90999%7CTGFR2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ90669%7CAVR2A_CHICK.for.1081350-1083542.23.fasta -t /tmp/maker_6B3o0i/23/2283742.1081350-1083542.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.1081350-1083542.sp%7CQ90669%7CAVR2A_CHICK.p.exonerate
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ05438%7CBMR1B_CHICK.for.1081320-1084827.23.fasta -t /tmp/maker_6B3o0i/23/2283742.1081320-1084827.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.1081320-1084827.sp%7CQ05438%7CBMR1B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ90670%7CAVR2B_CHICK.for.1081350-1083542.23.fasta -t /tmp/maker_6B3o0i/23/2283742.1081350-1083542.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.1081350-1083542.sp%7CQ90670%7CAVR2B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/23/sp%7CQ90ZK6%7CACVR1_CHICK.for.1081281-1084371.23.fasta -t /tmp/maker_6B3o0i/23/2283742.1081281-1084371.23.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/23/2283742.1081281-1084371.sp%7CQ90ZK6%7CACVR1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ9DGD1%7CMGT4C_CHICK.for.431748-433690.26.fasta -t /tmp/maker_6B3o0i/26/2283748.431748-433690.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.431748-433690.sp%7CQ9DGD1%7CMGT4C_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
choosing best annotation set
Choosing best annotations
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2283696.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/05/2283696//theVoid.2283696/1/2283696.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing chunk output
merging blast reports...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:33   current j:0
 j_size:33   current j:1
 j_size:33   current j:2
 j_size:33   current j:3
 j_size:33   current j:4
 j_size:33   current j:5
 j_size:33   current j:6
 j_size:33   current j:7
 j_size:33   current j:8
 j_size:33   current j:9
 j_size:33   current j:10
 j_size:33   current j:11
 j_size:33   current j:12
 j_size:33   current j:13
 j_size:33   current j:14
 j_size:33   current j:15
 j_size:33   current j:16
 j_size:33   current j:17
 j_size:33   current j:18
 j_size:33   current j:19
 j_size:33   current j:20
 j_size:33   current j:21
 j_size:33   current j:22
 j_size:33   current j:23
 j_size:33   current j:24
 j_size:33   current j:25
 j_size:33   current j:26
 j_size:33   current j:27
 j_size:33   current j:28
 j_size:33   current j:29
 j_size:33   current j:30
 j_size:33   current j:31
 j_size:33   current j:32
...finished clustering.
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284529
Length: 1287890
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing the chunk divide
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing ab-inits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
collecting blastx reports
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
merging blast reports...
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
running  blast search.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
deleted:0 hits
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
preparing evidence clusters for annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1 -pa 1
#-------------------------------#
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP02642%7CTNNT2_CHICK.for.612235-614935.26.fasta -t /tmp/maker_6B3o0i/26/2283748.612235-614935.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.612235-614935.sp%7CP02642%7CTNNT2_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP12620%7CTNNT3_CHICK.for.612799-614935.26.fasta -t /tmp/maker_6B3o0i/26/2283748.612799-614935.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.612799-614935.sp%7CP12620%7CTNNT3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP68246%7CTNNI2_CHICK.for.644168-645186.26.fasta -t /tmp/maker_6B3o0i/26/2283748.644168-645186.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.644168-645186.sp%7CP68246%7CTNNI2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP27673%7CTNNI3_CHICK.for.644201-645141.26.fasta -t /tmp/maker_6B3o0i/26/2283748.644201-645141.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.644201-645141.sp%7CP27673%7CTNNI3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP67966%7CCSRP1_CHICK.for.664779-672593.26.fasta -t /tmp/maker_6B3o0i/26/2283748.664779-672593.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.664779-672593.sp%7CP67966%7CCSRP1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP50460%7CCSRP2_CHICK.for.664399-672593.26.fasta -t /tmp/maker_6B3o0i/26/2283748.664399-672593.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.664399-672593.sp%7CP50460%7CCSRP2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
processing all repeats
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
re-running blast for edge cases...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/20/blastprep/db.1389776-1410522.for_blastx.fasta
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.1389776-1410522.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.1389776.1410522.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.1389776.1410522.0.db%2E1389776-1410522%2Efor_blastx%2Efasta.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
...finished
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
processing all repeats
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
re-running blast for edge cases...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/35/blastprep/db.71551-154993.for_blastx.fasta
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.71551-154993.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.71551.154993.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.71551.154993.0.db%2E71551-154993%2Efor_blastx%2Efasta.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
processing chunk output
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CF1NTD6%7CASCC3_CHICK.for.81151-145393.35.fasta -t /tmp/maker_6B3o0i/35/2284296.81151-145393.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284296.81151-145393.sp%7CF1NTD6%7CASCC3_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
collecting blastx repeatmasking
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/0/2283899.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
processing contig output
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
doing blastx of proteins
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
deleted:1 hits
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:2 hits
examining contents of the fasta file and run log



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284530
Length: 2584129
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
polishing proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP47191%7CSYT1_CHICK.for.861402-865348.26.fasta -t /tmp/maker_6B3o0i/26/2283748.861402-865348.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.861402-865348.sp%7CP47191%7CSYT1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ90922%7CNET1_CHICK.for.827377-838925.28.fasta -t /tmp/maker_6B3o0i/28/2283431.827377-838925.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.827377-838925.sp%7CQ90922%7CNET1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ90923%7CNET3_CHICK.for.827377-838886.28.fasta -t /tmp/maker_6B3o0i/28/2283431.827377-838886.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.827377-838886.sp%7CQ90923%7CNET3_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:1 now processing 0
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2283707.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F8/BD/2283707//theVoid.2283707/1/2283707.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
choosing best annotation set
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
merging blast reports...
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ7T0L4%7CTE2IP_CHICK.for.1640012-1641252.20.fasta -t /tmp/maker_6B3o0i/20/2283707.1640012-1641252.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2283707.1640012-1641252.sp%7CQ7T0L4%7CTE2IP_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ5ZI16%7CADAT1_CHICK.for.1663180-1688369.20.fasta -t /tmp/maker_6B3o0i/20/2283707.1663180-1688369.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2283707.1663180-1688369.sp%7CQ5ZI16%7CADAT1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CF1NNL1%7CTM231_CHICK.for.1706795-1712329.20.fasta -t /tmp/maker_6B3o0i/20/2283707.1706795-1712329.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2283707.1706795-1712329.sp%7CF1NNL1%7CTM231_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
processing chunk output
doing blastx repeats
cleaning blastx...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/0/2283431.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:29   current j:0
 j_size:29   current j:1
 j_size:29   current j:2
 j_size:29   current j:3
 j_size:29   current j:4
 j_size:29   current j:5
 j_size:29   current j:6
 j_size:29   current j:7
 j_size:29   current j:8
 j_size:29   current j:9
 j_size:29   current j:10
 j_size:29   current j:11
 j_size:29   current j:12
 j_size:29   current j:13
 j_size:29   current j:14
 j_size:29   current j:15
 j_size:29   current j:16
 j_size:29   current j:17
 j_size:29   current j:18
 j_size:29   current j:19
 j_size:29   current j:20
 j_size:29   current j:21
 j_size:29   current j:22
 j_size:29   current j:23
 j_size:29   current j:24
 j_size:29   current j:25
 j_size:29   current j:26
 j_size:29   current j:27
 j_size:29   current j:28
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing the chunk divide
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/0/2283748.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing chunk output
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
preparing masked sequence
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
gathering ab-init output files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:3 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
doing blastx repeats
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:5 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/0/2283464.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
preparing evidence clusters for annotations
running  blast search.
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
processing chunk output
deleted:0 hits
examining contents of the fasta file and run log
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
polishing proteins



--Next Contig--

running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CO73691%7CEGR1_CHICK.for.1019329-1020359.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1019329-1020359.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1019329-1020359.sp%7CO73691%7CEGR1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
cleaning blastx...
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284542
Length: 1554857
#---------------------------------------------------------------------


deleted:0 hits
deleted:0 hits
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx repeats
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:1 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
collecting blastx reports
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
merging blast reports...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:30   current j:0
 j_size:30   current j:1
 j_size:30   current j:2
 j_size:30   current j:3
 j_size:30   current j:4
 j_size:30   current j:5
 j_size:30   current j:6
 j_size:30   current j:7
 j_size:30   current j:8
 j_size:30   current j:9
 j_size:30   current j:10
 j_size:30   current j:11
 j_size:30   current j:12
 j_size:30   current j:13
 j_size:30   current j:14
 j_size:30   current j:15
 j_size:30   current j:16
 j_size:30   current j:17
 j_size:30   current j:18
 j_size:30   current j:19
 j_size:30   current j:20
 j_size:30   current j:21
 j_size:30   current j:22
 j_size:30   current j:23
 j_size:30   current j:24
 j_size:30   current j:25
 j_size:30   current j:26
 j_size:30   current j:27
 j_size:30   current j:28
 j_size:30   current j:29
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:3 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2283742.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/92/34/2283742//theVoid.2283742/1/2283742.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:2 hits
deleted:0 hits
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
prepare section files
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:2 hits
collecting blastx reports
deleted:1 hits
processing chunk output
deleted:0 hits
doing repeat masking
merging blast reports...
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing the chunk divide
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
polishing proteins
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ5F3R2%7CKDM5B_CHICK.for.1113349-1150333.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1113349-1150333.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1113349-1150333.sp%7CQ5F3R2%7CKDM5B_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing ab-inits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
gathering ab-init output files
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2 -pa 1
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ5ZJ23%7CASSY_CHICK.for.1110279-1137343.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1110279-1137343.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1110279-1137343.sp%7CQ5ZJ23%7CASSY_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:-3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing repeat masking
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:-4 hits
deleted:0 hits
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
choosing best annotation set
Choosing best annotations
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1 -pa 1
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
polishing proteins
polishing proteins
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09652%7CTBB4_CHICK.for.1202701-1209493.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202701-1209493.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202701-1209493.sp%7CP09652%7CTBB4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ9YH13%7CHXC8_CHICK.for.400-2206.19.fasta -t /tmp/maker_6B3o0i/19/2284058.400-2206.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.400-2206.sp%7CQ9YH13%7CHXC8_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP24341%7CHXD10_CHICK.for.1161-2173.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1161-2173.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1161-2173.sp%7CP24341%7CHXD10_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ05502%7CHHEX_CHICK.for.1200-2281.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1200-2281.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1200-2281.sp%7CQ05502%7CHHEX_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09244%7CTBB7_CHICK.for.1202746-1209493.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202746-1209493.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202746-1209493.sp%7CP09244%7CTBB7_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09645%7CTBA8_CHICK.for.1202701-1204717.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202701-1204717.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202701-1204717.sp%7CP09645%7CTBA8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ02814%7CHMD2_CHICK.for.1212-2173.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1212-2173.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1212-2173.sp%7CQ02814%7CHMD2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09642%7CTBA3_CHICK.for.1202722-1204720.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202722-1204720.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202722-1204720.sp%7CP09642%7CTBA3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP17278%7CHXD4_CHICK.for.1203-2245.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2245.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2245.sp%7CP17278%7CHXD4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP02552%7CTBA1_CHICK.for.1202728-1209379.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202728-1209379.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202728-1209379.sp%7CP02552%7CTBA1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP14839%7CHXB6_CHICK.for.1203-2233.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2233.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2233.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ6RFL5%7CBSH_CHICK.for.1200-2176.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1200-2176.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1200-2176.sp%7CQ6RFL5%7CBSH_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ6B3N0%7CHXA5_CHICK.for.19848-20851.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19848-20851.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19848-20851.sp%7CQ6B3N0%7CHXA5_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP24341%7CHXD10_CHICK.for.19836-20839.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19836-20839.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19836-20839.sp%7CP24341%7CHXD10_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09203%7CTBB1_CHICK.for.1202746-1209493.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202746-1209493.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202746-1209493.sp%7CP09203%7CTBB1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP08070%7CTBA2_CHICK.for.1202710-1209493.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202710-1209493.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202710-1209493.sp%7CP08070%7CTBA2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP79775%7CANF1_CHICK.for.19869-20848.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19869-20848.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19869-20848.sp%7CP79775%7CANF1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP13544%7CHXD1_CHICK.for.19878-20839.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19878-20839.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19878-20839.sp%7CP13544%7CHXD1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP14840%7CHXB4_CHICK.for.19025-20926.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19025-20926.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19025-20926.sp%7CP14840%7CHXB4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09206%7CTBB3_CHICK.for.1202746-1209493.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202746-1209493.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202746-1209493.sp%7CP09206%7CTBB3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP14839%7CHXB6_CHICK.for.19860-20875.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19860-20875.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19860-20875.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09653%7CTBB5_CHICK.for.1202746-1209493.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202746-1209493.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202746-1209493.sp%7CP09653%7CTBB5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ9W6D8%7CBARX1_CHICK.for.19869-20839.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19869-20839.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19869-20839.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP24341%7CHXD10_CHICK.for.50885-51882.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50885-51882.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50885-51882.sp%7CP24341%7CHXD10_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ98924%7CHXA9_CHICK.for.50909-51882.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51882.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51882.sp%7CQ98924%7CHXA9_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ90963%7CPRRX2_CHICK.for.50912-51891.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50912-51891.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50912-51891.sp%7CQ90963%7CPRRX2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP17278%7CHXD4_CHICK.for.50879-51879.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50879-51879.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50879-51879.sp%7CP17278%7CHXD4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09644%7CTBA5_CHICK.for.1202731-1209493.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202731-1209493.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202731-1209493.sp%7CP09644%7CTBA5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP09643%7CTBA4_CHICK.for.1202707-1204720.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202707-1204720.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202707-1204720.sp%7CP09643%7CTBA4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP14838%7CHXB5_CHICK.for.50891-51906.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50891-51906.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50891-51906.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP28362%7CMSX2_CHICK.for.50909-51915.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51915.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51915.sp%7CP28362%7CMSX2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP32882%7CTBB2_CHICK.for.1202746-1209493.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1202746-1209493.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1202746-1209493.sp%7CP32882%7CTBB2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ5ZKD9%7CKLH20_CHICK.for.1248212-1263554.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1248212-1263554.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1248212-1263554.sp%7CQ5ZKD9%7CKLH20_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 12
 ...processing 1 of 12
 ...processing 2 of 12
 ...processing 3 of 12
 ...processing 4 of 12
 ...processing 5 of 12
 ...processing 6 of 12
 ...processing 7 of 12
 ...processing 8 of 12
 ...processing 9 of 12
 ...processing 10 of 12
 ...processing 11 of 12
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 12
 ...processing 1 of 12
 ...processing 2 of 12
 ...processing 3 of 12
 ...processing 4 of 12
 ...processing 5 of 12
 ...processing 6 of 12
 ...processing 7 of 12
 ...processing 8 of 12
 ...processing 9 of 12
 ...processing 10 of 12
 ...processing 11 of 12
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
flattening protein clusters
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP15142%7CHM7X_CHICK.for.1203-2173.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2173.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2173.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP19601%7CSAX1_CHICK.for.1203-2179.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2179.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2179.sp%7CP19601%7CSAX1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ98924%7CHXA9_CHICK.for.1203-2179.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2179.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2179.sp%7CQ98924%7CHXA9_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP13544%7CHXD1_CHICK.for.1212-2173.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1212-2173.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1212-2173.sp%7CP13544%7CHXD1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP23459%7CHXD8_CHICK.for.439-2281.19.fasta -t /tmp/maker_6B3o0i/19/2284058.439-2281.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.439-2281.sp%7CP23459%7CHXD8_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP24340%7CHXD9_CHICK.for.1203-2173.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2173.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2173.sp%7CP24340%7CHXD9_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ9W6D8%7CBARX1_CHICK.for.1203-2173.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2173.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2173.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP15142%7CHM7X_CHICK.for.19845-20899.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19845-20899.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19845-20899.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP19601%7CSAX1_CHICK.for.19860-20845.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19860-20845.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19860-20845.sp%7CP19601%7CSAX1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ98924%7CHXA9_CHICK.for.19869-20848.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19869-20848.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19869-20848.sp%7CQ98924%7CHXA9_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ91975%7CDBX2_CHICK.for.19878-20836.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19878-20836.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19878-20836.sp%7CQ91975%7CDBX2_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP23459%7CHXD8_CHICK.for.19869-20863.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19869-20863.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19869-20863.sp%7CP23459%7CHXD8_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP24340%7CHXD9_CHICK.for.19869-20839.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19869-20839.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19869-20839.sp%7CP24340%7CHXD9_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ6B3N0%7CHXA5_CHICK.for.50885-51906.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50885-51906.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50885-51906.sp%7CQ6B3N0%7CHXA5_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ9PVY0%7CRX1_CHICK.for.50909-51879.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51879.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51879.sp%7CQ9PVY0%7CRX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ05437%7CPRRX1_CHICK.for.50912-51906.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50912-51906.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50912-51906.sp%7CQ05437%7CPRRX1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP13544%7CHXD1_CHICK.for.50897-51882.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50897-51882.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50897-51882.sp%7CP13544%7CHXD1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP14840%7CHXB4_CHICK.for.50882-51879.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50882-51879.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50882-51879.sp%7CP14840%7CHXB4_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP14839%7CHXB6_CHICK.for.50894-51879.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50894-51879.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50894-51879.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ6RFL5%7CBSH_CHICK.for.50906-51885.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50906-51885.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50906-51885.sp%7CQ6RFL5%7CBSH_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
collecting blastx repeatmasking
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
polishing proteins
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ5YLH5%7CHXA6_CHICK.for.1203-2221.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2221.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2221.sp%7CQ5YLH5%7CHXA6_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CP62167%7CNCS1_CHICK.for.1193712-1196433.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1193712-1196433.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1193712-1196433.sp%7CP62167%7CNCS1_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
doing blastx repeats
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ90VZ9%7CHXA7_CHICK.for.1185-2179.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1185-2179.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1185-2179.sp%7CQ90VZ9%7CHXA7_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP31259%7CHXB1_CHICK.for.1212-2245.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1212-2245.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1212-2245.sp%7CP31259%7CHXB1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CP62764%7CVISL1_CHICK.for.1195499-1196508.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1195499-1196508.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1195499-1196508.sp%7CP62764%7CVISL1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ91975%7CDBX2_CHICK.for.1203-2224.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1203-2224.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1203-2224.sp%7CQ91975%7CDBX2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP14838%7CHXB5_CHICK.for.1191-2179.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1191-2179.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1191-2179.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP23681%7CHXB8_CHICK.for.1188-2104.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1188-2104.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1188-2104.sp%7CP23681%7CHXB8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ9YH13%7CHXC8_CHICK.for.19875-20863.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19875-20863.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19875-20863.sp%7CQ9YH13%7CHXC8_CHICK.p.exonerate
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ5YLH5%7CHXA6_CHICK.for.19857-20860.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19857-20860.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19857-20860.sp%7CQ5YLH5%7CHXA6_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ90VZ9%7CHXA7_CHICK.for.19854-20848.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19854-20848.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19854-20848.sp%7CQ90VZ9%7CHXA7_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ02814%7CHMD2_CHICK.for.19878-20839.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19878-20839.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19878-20839.sp%7CQ02814%7CHMD2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP17278%7CHXD4_CHICK.for.19025-20941.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19025-20941.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19025-20941.sp%7CP17278%7CHXD4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP14838%7CHXB5_CHICK.for.19848-20893.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19848-20893.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19848-20893.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP17277%7CHXA4_CHICK.for.19839-20887.19.fasta -t /tmp/maker_6B3o0i/19/2284058.19839-20887.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.19839-20887.sp%7CP17277%7CHXA4_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP15142%7CHM7X_CHICK.for.50909-51870.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51870.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51870.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ90VZ9%7CHXA7_CHICK.for.50909-51918.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51918.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51918.sp%7CQ90VZ9%7CHXA7_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ02814%7CHMD2_CHICK.for.50909-51870.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51870.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51870.sp%7CQ02814%7CHMD2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ91975%7CDBX2_CHICK.for.50909-51891.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51891.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51891.sp%7CQ91975%7CDBX2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP23459%7CHXD8_CHICK.for.50909-51915.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51915.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51915.sp%7CP23459%7CHXD8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP24340%7CHXD9_CHICK.for.50909-51870.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50909-51870.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50909-51870.sp%7CP24340%7CHXD9_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ9W6D8%7CBARX1_CHICK.for.50906-51870.19.fasta -t /tmp/maker_6B3o0i/19/2284058.50906-51870.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.50906-51870.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
prepare section files
doing blastx repeats
running  blast search.
clustering transcripts into genes for annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Processing transcripts into genes
flattening protein clusters
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
processing chunk output
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:35   current j:0
 j_size:35   current j:1
 j_size:35   current j:2
 j_size:35   current j:3
 j_size:35   current j:4
 j_size:35   current j:5
 j_size:35   current j:6
 j_size:35   current j:7
 j_size:35   current j:8
 j_size:35   current j:9
 j_size:35   current j:10
 j_size:35   current j:11
 j_size:35   current j:12
 j_size:35   current j:13
 j_size:35   current j:14
 j_size:35   current j:15
 j_size:35   current j:16
 j_size:35   current j:17
 j_size:35   current j:18
 j_size:35   current j:19
 j_size:35   current j:20
 j_size:35   current j:21
 j_size:35   current j:22
 j_size:35   current j:23
 j_size:35   current j:24
 j_size:35   current j:25
 j_size:35   current j:26
 j_size:35   current j:27
 j_size:35   current j:28
 j_size:35   current j:29
 j_size:35   current j:30
 j_size:35   current j:31
 j_size:35   current j:32
 j_size:35   current j:33
 j_size:35   current j:34
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
flattening protein clusters
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/42/sp%7CQ90751%7CBMP2_CHICK.for.1487303-1491026.42.fasta -t /tmp/maker_6B3o0i/42/2283899.1487303-1491026.42.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/42/2283899.1487303-1491026.sp%7CQ90751%7CBMP2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/42/sp%7CQ90752%7CBMP4_CHICK.for.1487303-1491182.42.fasta -t /tmp/maker_6B3o0i/42/2283899.1487303-1491182.42.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/42/2283899.1487303-1491182.sp%7CQ90752%7CBMP4_CHICK.p.exonerate
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
deleted:0 hits
flattening protein clusters
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
prepare section files
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
annotating transcripts
running  blast search.
Making transcripts
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
deleted:0 hits
Preparing evidence for hint based annotation
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing contig output
deleted:0 hits
collecting blastx reports
deleted:0 hits
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
merging blast reports...
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284543
Length: 1410865
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
merging blast reports...
doing blastx repeats
doing repeat masking
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
gathering ab-init output files
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:2 hits
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
prepare section files
collecting blastx repeatmasking
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/0/2284296.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CQ8JJC0%7CZIC1_CHICK.for.916166-917220.35.fasta -t /tmp/maker_6B3o0i/35/2284296.916166-917220.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284296.916166-917220.sp%7CQ8JJC0%7CZIC1_CHICK.p.exonerate
#-------------------------------#
deleted:1 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CP55168%7CCCNC_CHICK.for.952624-968602.35.fasta -t /tmp/maker_6B3o0i/35/2284296.952624-968602.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284296.952624-968602.sp%7CP55168%7CCCNC_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:2 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CQ5ZKQ8%7CARL8A_CHICK.for.1561652-1567901.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1561652-1567901.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1561652-1567901.sp%7CQ5ZKQ8%7CARL8A_CHICK.p.exonerate
#-------------------------------#
collecting blastx reports
deleted:0 hits
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2283899.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/69/2283899//theVoid.2283899/1/2283899.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
polishing proteins
deleted:0 hits
processing chunk output
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ05437%7CPRRX1_CHICK.for.1542353-1544320.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1542353-1544320.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1542353-1544320.sp%7CQ05437%7CPRRX1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ90963%7CPRRX2_CHICK.for.1542353-1544380.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1542353-1544380.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1542353-1544380.sp%7CQ90963%7CPRRX2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CO73592%7CMIXL1_CHICK.for.1543395-1544377.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1543395-1544377.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1543395-1544377.sp%7CO73592%7CMIXL1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
prepare section files
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/42/sp%7CQ401C0%7CCNIH2_CHICK.for.1703368-1704335.42.fasta -t /tmp/maker_6B3o0i/42/2283899.1703368-1704335.42.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/42/2283899.1703368-1704335.sp%7CQ401C0%7CCNIH2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:2 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
choosing best annotation set
Choosing best annotations
flattening protein clusters
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
doing blastx repeats
deleted:0 hits
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing the chunk divide
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
doing blastx repeats
Calculating annotation quality statistics
doing blastx of proteins
doing blastx repeats
running  blast search.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2283748.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/9E/2283748//theVoid.2283748/1/2283748.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
flattening protein clusters
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
doing blastx repeats
Preparing evidence for hint based annotation
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
polishing proteins
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CO73705%7CCAC1A_CHICK.for.1700406-1703295.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1700406-1703295.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1700406-1703295.sp%7CO73705%7CCAC1A_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CO73706%7CCAC1B_CHICK.for.1700406-1703319.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1700406-1703319.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1700406-1703319.sp%7CO73706%7CCAC1B_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CO73707%7CCAC1C_CHICK.for.1700406-1703313.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1700406-1703313.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1700406-1703313.sp%7CO73707%7CCAC1C_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CO73700%7CCAC1D_CHICK.for.1694596-1749881.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1694596-1749881.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1694596-1749881.sp%7CO73700%7CCAC1D_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CO42398%7CCAC1S_CHICK.for.1700451-1711626.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1700451-1711626.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1700451-1711626.sp%7CO42398%7CCAC1S_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP00698%7CLYSC_CHICK.for.1756678-1757636.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1756678-1757636.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1756678-1757636.sp%7CP00698%7CLYSC_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP00708%7CLYSC_COLLI.for.1756681-1757636.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1756681-1757636.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1756681-1757636.sp%7CP00708%7CLYSC_COLLI.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/26/sp%7CP00703%7CLYSC_MELGA.for.1756678-1757636.26.fasta -t /tmp/maker_6B3o0i/26/2283748.1756678-1757636.26.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/26/2283748.1756678-1757636.sp%7CP00703%7CLYSC_MELGA.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
choosing best annotation set
Choosing best annotations
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:2 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
processing chunk output
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
prepare section files
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
prepare section files
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
choosing best annotation set
 j_size:24   current j:23
...finished clustering.
Choosing best annotations
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
processing chunk output
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing the chunk divide
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx of proteins
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
preparing evidence clusters for annotations
doing repeat masking
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284552
Length: 2668160
#---------------------------------------------------------------------


Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
setting up GFF3 output and fasta chunks
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
processing all repeats
in cluster::shadow_cluster...
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1 -pa 1
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284296.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/45/D7/2284296//theVoid.2284296/1/2284296.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
prepare section files
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
processing chunk output
merging blast reports...
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
merging blast reports...
doing blastx repeats
preparing evidence clusters for annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
collecting blastx repeatmasking
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing the chunk divide
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
flattening protein clusters
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
prepare section files
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
collecting blastx repeatmasking
prepare section files
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
flattening protein clusters
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing ab-inits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
annotating transcripts
Making transcripts
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
gathering ab-init output files
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
collecting blastx repeatmasking
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:-1 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
merging blast reports...
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2283431.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/79/2283431//theVoid.2283431/1/2283431.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
collecting blastx reports
Preparing evidence for hint based annotation
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ5ZMA3%7CRBM24_CHICK.for.628346-629322.19.fasta -t /tmp/maker_6B3o0i/19/2284058.628346-629322.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.628346-629322.sp%7CQ5ZMA3%7CRBM24_CHICK.p.exonerate
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ5ZJX4%7CRBM38_CHICK.for.628346-629322.19.fasta -t /tmp/maker_6B3o0i/19/2284058.628346-629322.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.628346-629322.sp%7CQ5ZJX4%7CRBM38_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ5ZL67%7CNF2L1_CHICK.for.650164-655635.19.fasta -t /tmp/maker_6B3o0i/19/2284058.650164-655635.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.650164-655635.sp%7CQ5ZL67%7CNF2L1_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
re-running blast for edge cases...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
doing blastx of proteins
Preparing evidence for hint based annotation
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/29/blastprep/db.1784702-1830577.for_blastx.fasta
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CP52826%7CCACP_COLLI.for.1813263-1824723.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1813263-1824723.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1813263-1824723.sp%7CP52826%7CCACP_COLLI.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.1784702-1830577.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.1784702.1830577.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.1784702.1830577.0.db%2E1784702-1830577%2Efor_blastx%2Efasta.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ90YJ9%7CCLAT_CHICK.for.1813344-1824696.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1813344-1824696.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1813344-1824696.sp%7CQ90YJ9%7CCLAT_CHICK.p.exonerate
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ5ZIR1%7CSHLB1_CHICK.for.1881723-1885312.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1881723-1885312.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1881723-1885312.sp%7CQ5ZIR1%7CSHLB1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ5ZJ81%7CSHLB2_CHICK.for.1881723-1884506.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1881723-1884506.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1881723-1884506.sp%7CQ5ZJ81%7CSHLB2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
...finished
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ5ZIR1%7CSHLB1_CHICK.for.1895792-1899418.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1895792-1899418.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1895792-1899418.sp%7CQ5ZIR1%7CSHLB1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CQ5ZJ81%7CSHLB2_CHICK.for.1895783-1899418.28.fasta -t /tmp/maker_6B3o0i/28/2283431.1895783-1899418.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2283431.1895783-1899418.sp%7CQ5ZJ81%7CSHLB2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP16924%7CP4HA1_CHICK.for.1794302-1820977.29.fasta -t /tmp/maker_6B3o0i/29/2283464.1794302-1820977.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2283464.1794302-1820977.sp%7CP16924%7CP4HA1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ5ZLK5%7CP4HA2_CHICK.for.1794302-1820441.29.fasta -t /tmp/maker_6B3o0i/29/2283464.1794302-1820441.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2283464.1794302-1820441.sp%7CQ5ZLK5%7CP4HA2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CO73885%7CHSP7C_CHICK.for.59223-62885.41.fasta -t /tmp/maker_6B3o0i/41/2283556.59223-62885.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.59223-62885.sp%7CO73885%7CHSP7C_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZM98%7CGRP75_CHICK.for.59669-62684.41.fasta -t /tmp/maker_6B3o0i/41/2283556.59669-62684.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.59669-62684.sp%7CQ5ZM98%7CGRP75_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
clustering transcripts into genes for annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CE1C2P3%7CHSP7E_CHICK.for.59660-61600.41.fasta -t /tmp/maker_6B3o0i/41/2283556.59660-61600.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.59660-61600.sp%7CE1C2P3%7CHSP7E_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing the chunk divide
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ90593%7CGRP78_CHICK.for.59226-62933.41.fasta -t /tmp/maker_6B3o0i/41/2283556.59226-62933.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.59226-62933.sp%7CQ90593%7CGRP78_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZLK7%7CHYOU1_CHICK.for.59663-61585.41.fasta -t /tmp/maker_6B3o0i/41/2283556.59663-61585.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.59663-61585.sp%7CQ5ZLK7%7CHYOU1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP08106%7CHSP70_CHICK.for.59226-62879.41.fasta -t /tmp/maker_6B3o0i/41/2283556.59226-62879.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.59226-62879.sp%7CP08106%7CHSP70_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZJ37%7CRABEK_CHICK.for.63866-66765.41.fasta -t /tmp/maker_6B3o0i/41/2283556.63866-66765.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.63866-66765.sp%7CQ5ZJ37%7CRABEK_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP62207%7CPP1B_CHICK.for.68644-71974.41.fasta -t /tmp/maker_6B3o0i/41/2283556.68644-71974.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.68644-71974.sp%7CP62207%7CPP1B_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP48463%7CPP2AA_CHICK.for.68623-71983.41.fasta -t /tmp/maker_6B3o0i/41/2283556.68623-71983.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.68623-71983.sp%7CP48463%7CPP2AA_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
total clusters:3 now processing 0
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
clustering transcripts into genes for annotations
running  blast search.
Processing transcripts into genes
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/0/2284162.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
merging blast reports...
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:1 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2283464.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/86/C2/2283464//theVoid.2283464/1/2283464.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
collecting blastx reports
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
processing chunk output
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ98TF7%7CRL35_CHICK.for.176430-178603.41.fasta -t /tmp/maker_6B3o0i/41/2283556.176430-178603.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.176430-178603.sp%7CQ98TF7%7CRL35_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
doing blastx repeats
running  blast search.
clustering transcripts into genes for annotations
Processing transcripts into genes
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
adding statistics to annotations
Calculating annotation quality statistics
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
doing blastx repeats
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
processing the chunk divide
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
deleted:0 hits
prepare section files
choosing best annotation set
Choosing best annotations
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1 -pa 1
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Preparing evidence for hint based annotation
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
choosing best annotation set
Choosing best annotations
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
processing chunk output
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing contig output
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284554
Length: 1238774
#---------------------------------------------------------------------


deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
choosing best annotation set
Choosing best annotations
setting up GFF3 output and fasta chunks
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
doing repeat masking
collecting blastx reports
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx reports
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/0/2284058.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 12
 ...processing 1 of 12
 ...processing 2 of 12
 ...processing 3 of 12
 ...processing 4 of 12
 ...processing 5 of 12
 ...processing 6 of 12
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 ...processing 7 of 12
deleted:0 hits
 ...processing 8 of 12
 ...processing 9 of 12
 ...processing 10 of 12
 ...processing 11 of 12
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284571
Length: 2309371
#---------------------------------------------------------------------


deleted:0 hits
setting up GFF3 output and fasta chunks
merging blast reports...
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
clustering transcripts into genes for annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
running  blast search.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
processing chunk output
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
collecting blastx repeatmasking
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
flattening protein clusters
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
polishing proteins
preparing evidence clusters for annotations
doing blastx repeats
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
preparing masked sequence
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CO42101%7CNR5A2_CHICK.for.327576-348245.41.fasta -t /tmp/maker_6B3o0i/41/2283556.327576-348245.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.327576-348245.sp%7CO42101%7CNR5A2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
cleaning blastx...
deleted:0 hits
merging blast reports...
merging blast reports...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
in cluster::shadow_cluster...
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP67881%7CCYC_CHICK.for.1063625-1066115.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1063625-1066115.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1063625-1066115.sp%7CP67881%7CCYC_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/5/sp%7CO13154%7CPACN2_CHICK.for.809644-813740.5.fasta -t /tmp/maker_6B3o0i/5/2284439.809644-813740.5.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/5/2284439.809644-813740.sp%7CO13154%7CPACN2_CHICK.p.exonerate
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
preparing masked sequence
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP00021%7CCYC_COLLI.for.1063625-1066115.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1063625-1066115.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1063625-1066115.sp%7CP00021%7CCYC_COLLI.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/5/sp%7CO13154%7CPACN2_CHICK.for.827985-837535.5.fasta -t /tmp/maker_6B3o0i/5/2284439.827985-837535.5.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/5/2284439.827985-837535.sp%7CO13154%7CPACN2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP67882%7CCYC_MELGA.for.1063625-1066115.19.fasta -t /tmp/maker_6B3o0i/19/2284058.1063625-1066115.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284058.1063625-1066115.sp%7CP67882%7CCYC_MELGA.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
flattening protein clusters
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
gathering ab-init output files
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
processing all repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
prepare section files
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing chunk output
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
deleted:0 hits
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx repeats
 ...processing 0 of 5
 ...processing 1 of 5
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
 ...processing 2 of 5
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 3 of 5
 ...processing 4 of 5
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
doing blastx repeats
running  blast search.
 ...processing 6 of 8
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
 ...processing 7 of 8
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
collecting blastx reports
Preparing evidence for hint based annotation
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
deleted:0 hits
doing blastx repeats
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284162.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/27/5F/2284162//theVoid.2284162/1/2284162.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/0/2284439.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
collecting blastx reports
choosing best annotation set
Choosing best annotations
collecting blastx reports
deleted:0 hits
merging blast reports...
prepare section files
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
processing chunk output
deleted:0 hits



--Next Contig--

deleted:0 hits
prepare section files
deleted:0 hits
flattening protein clusters
flattening protein clusters
doing repeat masking
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284607
Length: 2849260
#---------------------------------------------------------------------


doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
merging blast reports...
setting up GFF3 output and fasta chunks
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
processing the chunk divide
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
processing chunk output
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:2 hits
doing repeat masking
doing blastx of proteins
running  blast search.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
deleted:0 hits
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/0/2284256.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
prepare section files
deleted:0 hits
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/5/sp%7CQ5ZHX7%7CNB5R2_CHICK.for.1020692-1023105.5.fasta -t /tmp/maker_6B3o0i/5/2284439.1020692-1023105.5.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/5/2284439.1020692-1023105.sp%7CQ5ZHX7%7CNB5R2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
processing all repeats
in cluster::shadow_cluster...
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
flattening protein clusters
doing blastx of proteins
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
clustering transcripts into genes for annotations
collecting blastx reports
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
running  blast search.
Choosing best annotations
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:4 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:8 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
preparing evidence clusters for annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Preparing evidence for hint based annotation
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ8UVJ7%7CCDHR1_CHICK.for.242573-289666.13.fasta -t /tmp/maker_6B3o0i/13/2284451.242573-289666.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.242573-289666.sp%7CQ8UVJ7%7CCDHR1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:10 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284616
Length: 2212613
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:8 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
preparing ab-inits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:3 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
merging blast reports...
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
gathering ab-init output files
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:8 hits
doing repeat masking
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1 -pa 1
#-------------------------------#
doing blastx of proteins
polishing proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ90881%7CLHX9_CHICK.for.671424-680155.41.fasta -t /tmp/maker_6B3o0i/41/2283556.671424-680155.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.671424-680155.sp%7CQ90881%7CLHX9_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
cleaning blastx...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:9 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:11 hits
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP07228%7CITB1_CHICK.for.625828-628219.12.fasta -t /tmp/maker_6B3o0i/12/2284110.625828-628219.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.625828-628219.sp%7CP07228%7CITB1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
cleaning blastx...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:14 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:10 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284058.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/82/05/2284058//theVoid.2284058/1/2284058.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
running  blast search.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
collecting blastx reports
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
flattening protein clusters
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing the chunk divide
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 9
 ...processing 1 of 9
 ...processing 2 of 9
 ...processing 3 of 9
 ...processing 4 of 9
 ...processing 5 of 9
 ...processing 6 of 9
 ...processing 7 of 9
 ...processing 8 of 9
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
doing blastx repeats
 ...processing 3 of 8
 ...processing 4 of 8
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
total clusters:3 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
 ...processing 0 of 9
 ...processing 1 of 9
 ...processing 2 of 9
 ...processing 3 of 9
 ...processing 4 of 9
 ...processing 5 of 9
 ...processing 6 of 9
 ...processing 7 of 9
 ...processing 8 of 9
total clusters:3 now processing 0
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
in cluster::shadow_cluster...
...finished clustering.
merging blast reports...
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
flattening protein clusters
annotating transcripts
Making transcripts
 ...processing 0 of 13
 ...processing 1 of 13
 ...processing 2 of 13
 ...processing 3 of 13
 ...processing 4 of 13
 ...processing 5 of 13
 ...processing 6 of 13
 ...processing 7 of 13
 ...processing 8 of 13
 ...processing 9 of 13
 ...processing 10 of 13
 ...processing 11 of 13
 ...processing 12 of 13
deleted:0 hits
processing contig output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
 ...processing 0 of 9
 ...processing 1 of 9
 ...processing 2 of 9
 ...processing 3 of 9
 ...processing 4 of 9
 ...processing 5 of 9
 ...processing 6 of 9
 ...processing 7 of 9
 ...processing 8 of 9
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284622
Length: 1278201
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:11 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/5/sp%7CQ9I8T7%7CBMAL1_CHICK.for.1247776-1258549.5.fasta -t /tmp/maker_6B3o0i/5/2284439.1247776-1258549.5.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/5/2284439.1247776-1258549.sp%7CQ9I8T7%7CBMAL1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/5/sp%7CQ8QGQ7%7CBMAL2_CHICK.for.1229674-1266499.5.fasta -t /tmp/maker_6B3o0i/5/2284439.1229674-1266499.5.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/5/2284439.1229674-1266499.sp%7CQ8QGQ7%7CBMAL2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
polishing proteins
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP50211%7CISL1_CHICK.for.694418-696409.41.fasta -t /tmp/maker_6B3o0i/41/2283556.694418-696409.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.694418-696409.sp%7CP50211%7CISL1_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ90881%7CLHX9_CHICK.for.694226-696445.41.fasta -t /tmp/maker_6B3o0i/41/2283556.694226-696445.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.694226-696445.sp%7CQ90881%7CLHX9_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP53412%7CLHX3_CHICK.for.694406-696406.41.fasta -t /tmp/maker_6B3o0i/41/2283556.694406-696406.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.694406-696406.sp%7CP53412%7CLHX3_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP53410%7CISL2_CHICK.for.694436-696367.41.fasta -t /tmp/maker_6B3o0i/41/2283556.694436-696367.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.694436-696367.sp%7CP53410%7CISL2_CHICK.p.exonerate
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP53411%7CLHX1_CHICK.for.694427-696403.41.fasta -t /tmp/maker_6B3o0i/41/2283556.694427-696403.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.694427-696403.sp%7CP53411%7CLHX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
deleted:10 hits
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:8 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ90YJ9%7CCLAT_CHICK.for.413698-441728.13.fasta -t /tmp/maker_6B3o0i/13/2284451.413698-441728.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.413698-441728.sp%7CQ90YJ9%7CCLAT_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:14 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
running  blast search.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx repeatmasking
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:30   current j:0
 j_size:30   current j:1
 j_size:30   current j:2
 j_size:30   current j:3
 j_size:30   current j:4
 j_size:30   current j:5
 j_size:30   current j:6
 j_size:30   current j:7
 j_size:30   current j:8
 j_size:30   current j:9
 j_size:30   current j:10
 j_size:30   current j:11
 j_size:30   current j:12
 j_size:30   current j:13
 j_size:30   current j:14
 j_size:30   current j:15
 j_size:30   current j:16
 j_size:30   current j:17
 j_size:30   current j:18
 j_size:30   current j:19
 j_size:30   current j:20
 j_size:30   current j:21
 j_size:30   current j:22
 j_size:30   current j:23
 j_size:30   current j:24
 j_size:30   current j:25
 j_size:30   current j:26
 j_size:30   current j:27
 j_size:30   current j:28
 j_size:30   current j:29
...finished clustering.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CP63283%7CUBC9_CHICK.for.115255-121778.8.fasta -t /tmp/maker_6B3o0i/8/2284243.115255-121778.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284243.115255-121778.sp%7CP63283%7CUBC9_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:8 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1 -pa 1
#-------------------------------#
preparing masked sequence
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:7 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284439.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2B/69/2284439//theVoid.2284439/1/2284439.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
doing blastx of proteins
doing blastx of proteins
in cluster::shadow_cluster...
prepare section files
running  blast search.
running  blast search.
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284642
Length: 2757973
#---------------------------------------------------------------------


in cluster::shadow_cluster...
doing blastx repeats
doing repeat masking
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1 -pa 1
#-------------------------------#
prepare section files
setting up GFF3 output and fasta chunks
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
annotating transcripts
Making transcripts
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
processing the chunk divide
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
adding statistics to annotations
Calculating annotation quality statistics
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
preparing evidence clusters for annotations
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
prepare section files
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing masked sequence
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
prepare section files
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
choosing best annotation set
Choosing best annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
flattening protein clusters
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
processing chunk output
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/0/2284110.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP15575%7CB3AT_CHICK.for.925616-939940.12.fasta -t /tmp/maker_6B3o0i/12/2284110.925616-939940.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.925616-939940.sp%7CP15575%7CB3AT_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ5F479%7CS11IP_CHICK.for.961910-979223.12.fasta -t /tmp/maker_6B3o0i/12/2284110.961910-979223.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.961910-979223.sp%7CQ5F479%7CS11IP_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284256.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/80/43/2284256//theVoid.2284256/1/2284256.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/0/2283556.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/1/2284120.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
prepare section files
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing the chunk divide
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1 -pa 1
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
deleted:0 hits
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:39   current j:0
 j_size:39   current j:1
 j_size:39   current j:2
 j_size:39   current j:3
 j_size:39   current j:4
 j_size:39   current j:5
 j_size:39   current j:6
 j_size:39   current j:7
 j_size:39   current j:8
 j_size:39   current j:9
 j_size:39   current j:10
 j_size:39   current j:11
 j_size:39   current j:12
 j_size:39   current j:13
 j_size:39   current j:14
 j_size:39   current j:15
 j_size:39   current j:16
 j_size:39   current j:17
 j_size:39   current j:18
 j_size:39   current j:19
 j_size:39   current j:20
 j_size:39   current j:21
 j_size:39   current j:22
 j_size:39   current j:23
 j_size:39   current j:24
 j_size:39   current j:25
 j_size:39   current j:26
 j_size:39   current j:27
 j_size:39   current j:28
 j_size:39   current j:29
 j_size:39   current j:30
 j_size:39   current j:31
 j_size:39   current j:32
 j_size:39   current j:33
 j_size:39   current j:34
 j_size:39   current j:35
 j_size:39   current j:36
 j_size:39   current j:37
 j_size:39   current j:38
...finished clustering.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
flattening protein clusters
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
gathering ab-init output files
prepare section files
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:4 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
doing blastx repeats
doing blastx of proteins
running  blast search.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
preparing evidence clusters for annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:5 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:6 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
running  blast search.
processing chunk output
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
processing chunk output
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx of proteins
flattening protein clusters
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing evidence clusters for annotations
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
polishing proteins
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
doing repeat masking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CO93533%7CCXB6_CHICK.for.991443-992995.12.fasta -t /tmp/maker_6B3o0i/12/2284110.991443-992995.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.991443-992995.sp%7CO93533%7CCXB6_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP18860%7CCXA5_CHICK.for.991449-993199.12.fasta -t /tmp/maker_6B3o0i/12/2284110.991449-993199.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.991449-993199.sp%7CP18860%7CCXA5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP36381%7CCXA8_CHICK.for.991449-993031.12.fasta -t /tmp/maker_6B3o0i/12/2284110.991449-993031.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.991449-993031.sp%7CP36381%7CCXA8_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP14154%7CCXA1_CHICK.for.991449-993145.12.fasta -t /tmp/maker_6B3o0i/12/2284110.991449-993145.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.991449-993145.sp%7CP14154%7CCXA1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP29415%7CCXA3_CHICK.for.991449-993052.12.fasta -t /tmp/maker_6B3o0i/12/2284110.991449-993052.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.991449-993052.sp%7CP29415%7CCXA3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP18861%7CCXG1_CHICK.for.991443-993331.12.fasta -t /tmp/maker_6B3o0i/12/2284110.991443-993331.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.991443-993331.sp%7CP18861%7CCXG1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP43031%7CINHA_CHICK.for.994918-997393.12.fasta -t /tmp/maker_6B3o0i/12/2284110.994918-997393.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.994918-997393.sp%7CP43031%7CINHA_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0 -pa 1
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ1XA76%7CASIC1_CHICK.for.1045376-1049543.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1045376-1049543.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1045376-1049543.sp%7CQ1XA76%7CASIC1_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
cleaning blastx...
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:3 now processing 0
total clusters:3 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ9PWA3%7CGRIN2_CHICK.for.732542-734874.13.fasta -t /tmp/maker_6B3o0i/13/2284451.732542-734874.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.732542-734874.sp%7CQ9PWA3%7CGRIN2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284644
Length: 1606975
#---------------------------------------------------------------------


deleted:0 hits
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
flattening protein clusters
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
merging blast reports...
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
doing blastx repeats
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
clustering transcripts into genes for annotations
Processing transcripts into genes
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/2/2283926.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
prepare section files
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
deleted:5 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
processing all repeats
in cluster::shadow_cluster...
collecting blastx repeatmasking
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing masked sequence
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
preparing ab-inits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ1XA76%7CASIC1_CHICK.for.1111290-1112713.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1111290-1112713.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1111290-1112713.sp%7CQ1XA76%7CASIC1_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP56276%7CMYLK_MELGA.for.1149718-1150652.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1149718-1150652.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1149718-1150652.sp%7CP56276%7CMYLK_MELGA.p.exonerate
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP02542%7CDESM_CHICK.for.1181367-1186711.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1181367-1186711.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1181367-1186711.sp%7CP02542%7CDESM_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ6PVZ1%7CK1C14_CHICK.for.1181901-1184203.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1181901-1184203.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1181901-1184203.sp%7CQ6PVZ1%7CK1C14_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CO93532%7CK2CO_CHICK.for.1181880-1186474.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1181880-1186474.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1181880-1186474.sp%7CO93532%7CK2CO_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP14732%7CLMNB2_CHICK.for.1181895-1186474.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1181895-1186474.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1181895-1186474.sp%7CP14732%7CLMNB2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09654%7CVIME_CHICK.for.1181895-1186750.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1181895-1186750.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1181895-1186750.sp%7CP09654%7CVIME_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP16053%7CNFM_CHICK.for.1181895-1186723.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1181895-1186723.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1181895-1186723.sp%7CP16053%7CNFM_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CP00368%7CDHE3_CHICK.for.865267-883189.13.fasta -t /tmp/maker_6B3o0i/13/2284451.865267-883189.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.865267-883189.sp%7CP00368%7CDHE3_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
flattening protein clusters
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
collecting blastx reports
prepare section files
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CQ5ZLX4%7CARHG3_CHICK.for.840233-851588.1.fasta -t /tmp/maker_6B3o0i/1/2284232.840233-851588.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.840233-851588.sp%7CQ5ZLX4%7CARHG3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
collecting blastx reports
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
flattening protein clusters
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
flattening protein clusters
 ...processing 2 of 4
 ...processing 3 of 4
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
deleted:0 hits
prepare section files
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
re-running blast for edge cases...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/41/blastprep/db.1185831-1231224.for_blastx.fasta
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.1185831-1231224.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.1185831.1231224.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.1185831.1231224.0.db%2E1185831-1231224%2Efor_blastx%2Efasta.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZIL4%7CSTRBP_CHICK.for.1195431-1221624.41.fasta -t /tmp/maker_6B3o0i/41/2283556.1195431-1221624.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.1195431-1221624.sp%7CQ5ZIL4%7CSTRBP_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZJ17%7CRBG1L_CHICK.for.1268415-1280048.41.fasta -t /tmp/maker_6B3o0i/41/2283556.1268415-1280048.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.1268415-1280048.sp%7CQ5ZJ17%7CRBG1L_CHICK.p.exonerate
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
processing contig output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/0/2284451.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
prepare section files
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284647
Length: 1347408
#---------------------------------------------------------------------


prepare section files
doing blastx repeats
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ90669%7CAVR2A_CHICK.for.965462-967991.13.fasta -t /tmp/maker_6B3o0i/13/2284451.965462-967991.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.965462-967991.sp%7CQ90669%7CAVR2A_CHICK.p.exonerate
#-------------------------------#
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP02552%7CTBA1_CHICK.for.1236291-1246219.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236291-1246219.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236291-1246219.sp%7CP02552%7CTBA1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ05438%7CBMR1B_CHICK.for.963372-968009.13.fasta -t /tmp/maker_6B3o0i/13/2284451.963372-968009.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.963372-968009.sp%7CQ05438%7CBMR1B_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ90670%7CAVR2B_CHICK.for.966398-967991.13.fasta -t /tmp/maker_6B3o0i/13/2284451.966398-967991.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.966398-967991.sp%7CQ90670%7CAVR2B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09653%7CTBB5_CHICK.for.1236177-1246204.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236177-1246204.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236177-1246204.sp%7CP09653%7CTBB5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ90ZK6%7CACVR1_CHICK.for.963381-968009.13.fasta -t /tmp/maker_6B3o0i/13/2284451.963381-968009.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.963381-968009.sp%7CQ90ZK6%7CACVR1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP08070%7CTBA2_CHICK.for.1236177-1246240.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236177-1246240.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236177-1246240.sp%7CP08070%7CTBA2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/0/2284232.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing chunk output
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09207%7CTBB6_CHICK.for.1236535-1246246.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236535-1246246.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236535-1246246.sp%7CP09207%7CTBB6_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09642%7CTBA3_CHICK.for.1236870-1246234.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236870-1246234.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236870-1246234.sp%7CP09642%7CTBA3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09244%7CTBB7_CHICK.for.1236177-1246204.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236177-1246204.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236177-1246204.sp%7CP09244%7CTBB7_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09643%7CTBA4_CHICK.for.1236870-1246243.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236870-1246243.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236870-1246243.sp%7CP09643%7CTBA4_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09644%7CTBA5_CHICK.for.1236177-1246222.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236177-1246222.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236177-1246222.sp%7CP09644%7CTBA5_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09645%7CTBA8_CHICK.for.1236873-1246246.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236873-1246246.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236873-1246246.sp%7CP09645%7CTBA8_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP32882%7CTBB2_CHICK.for.1236177-1246204.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236177-1246204.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236177-1246204.sp%7CP32882%7CTBB2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP09652%7CTBB4_CHICK.for.1236177-1246243.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1236177-1246243.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1236177-1246243.sp%7CP09652%7CTBB4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
flattening protein clusters
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 11
 ...processing 1 of 11
 ...processing 2 of 11
 ...processing 3 of 11
 ...processing 4 of 11
 ...processing 5 of 11
 ...processing 6 of 11
 ...processing 7 of 11
 ...processing 8 of 11
 ...processing 9 of 11
 ...processing 10 of 11
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 11
 ...processing 1 of 11
 ...processing 2 of 11
 ...processing 3 of 11
 ...processing 4 of 11
 ...processing 5 of 11
 ...processing 6 of 11
 ...processing 7 of 11
 ...processing 8 of 11
 ...processing 9 of 11
 ...processing 10 of 11
total clusters:2 now processing 0
 ...processing 0 of 11
 ...processing 1 of 11
 ...processing 2 of 11
 ...processing 3 of 11
 ...processing 4 of 11
 ...processing 5 of 11
 ...processing 6 of 11
 ...processing 7 of 11
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
 ...processing 8 of 11
 ...processing 9 of 11
 ...processing 10 of 11
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:5 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:3 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:3 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:-1 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZJ17%7CRBG1L_CHICK.for.1314766-1332805.41.fasta -t /tmp/maker_6B3o0i/41/2283556.1314766-1332805.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.1314766-1332805.sp%7CQ5ZJ17%7CRBG1L_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
doing blastx of proteins
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
prepare section files
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ5ZJH7%7CCNPD1_CHICK.for.1311073-1317536.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1311073-1317536.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1311073-1317536.sp%7CQ5ZJH7%7CCNPD1_CHICK.p.exonerate
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing chunk output
doing blastx repeats
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CQ7T2L7%7CI17RD_CHICK.for.1047442-1051662.1.fasta -t /tmp/maker_6B3o0i/1/2284232.1047442-1051662.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.1047442-1051662.sp%7CQ7T2L7%7CI17RD_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
cleaning blastx...
doing blastx of proteins
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CQ7T2L7%7CI17RD_CHICK.for.1064898-1074985.1.fasta -t /tmp/maker_6B3o0i/1/2284232.1064898-1074985.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.1064898-1074985.sp%7CQ7T2L7%7CI17RD_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing contig output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/2/2283486.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284669
Length: 1647466
#---------------------------------------------------------------------


deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:29   current j:0
 j_size:29   current j:1
 j_size:29   current j:2
 j_size:29   current j:3
 j_size:29   current j:4
 j_size:29   current j:5
 j_size:29   current j:6
 j_size:29   current j:7
 j_size:29   current j:8
 j_size:29   current j:9
 j_size:29   current j:10
 j_size:29   current j:11
 j_size:29   current j:12
 j_size:29   current j:13
 j_size:29   current j:14
 j_size:29   current j:15
 j_size:29   current j:16
 j_size:29   current j:17
 j_size:29   current j:18
 j_size:29   current j:19
 j_size:29   current j:20
 j_size:29   current j:21
 j_size:29   current j:22
 j_size:29   current j:23
 j_size:29   current j:24
 j_size:29   current j:25
 j_size:29   current j:26
 j_size:29   current j:27
 j_size:29   current j:28
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
doing repeat masking
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:3 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP27607%7CPGH2_CHICK.for.1434746-1440957.41.fasta -t /tmp/maker_6B3o0i/41/2283556.1434746-1440957.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.1434746-1440957.sp%7CP27607%7CPGH2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
collecting blastx reports
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
deleted:2 hits
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:2 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/1/2284220.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ679P3%7CPDLI7_CHICK.for.1104085-1110451.13.fasta -t /tmp/maker_6B3o0i/13/2284451.1104085-1110451.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284451.1104085-1110451.sp%7CQ679P3%7CPDLI7_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
deleted:0 hits
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ98938%7CIHH_CHICK.for.1380076-1391233.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1380076-1391233.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1380076-1391233.sp%7CQ98938%7CIHH_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ91035%7CSHH_CHICK.for.1380076-1391218.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1380076-1391218.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1380076-1391218.sp%7CQ91035%7CSHH_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP15142%7CHM7X_CHICK.for.1415518-1416479.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1415518-1416479.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1415518-1416479.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP14838%7CHXB5_CHICK.for.1415524-1416479.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1415524-1416479.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1415524-1416479.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP14839%7CHXB6_CHICK.for.1415533-1416479.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1415533-1416479.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1415533-1416479.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CP79775%7CANF1_CHICK.for.1152356-1155118.1.fasta -t /tmp/maker_6B3o0i/1/2284232.1152356-1155118.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.1152356-1155118.sp%7CP79775%7CANF1_CHICK.p.exonerate
#-------------------------------#
collecting blastx repeatmasking
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CP32046%7CRL37A_CHICK.for.1173266-1174263.1.fasta -t /tmp/maker_6B3o0i/1/2284232.1173266-1174263.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.1173266-1174263.sp%7CP32046%7CRL37A_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
preparing masked sequence
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:-2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
gathering ab-init output files
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:-1 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CB5FYQ0%7CARL3_TAEGU.for.338952-339901.22.fasta -t /tmp/maker_6B3o0i/22/2284260.338952-339901.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.338952-339901.sp%7CB5FYQ0%7CARL3_TAEGU.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CP49702%7CARF5_CHICK.for.338952-344857.22.fasta -t /tmp/maker_6B3o0i/22/2284260.338952-344857.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.338952-344857.sp%7CP49702%7CARF5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CP26990%7CARF6_CHICK.for.338952-344857.22.fasta -t /tmp/maker_6B3o0i/22/2284260.338952-344857.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.338952-344857.sp%7CP26990%7CARF6_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP53412%7CLHX3_CHICK.for.1504077-1505122.41.fasta -t /tmp/maker_6B3o0i/41/2283556.1504077-1505122.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.1504077-1505122.sp%7CP53412%7CLHX3_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/0/2284243.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284110.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/63/63/2284110//theVoid.2284110/1/2284110.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CQ5ZJ66%7CSYEM_CHICK.for.947661-960303.8.fasta -t /tmp/maker_6B3o0i/8/2284243.947661-960303.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284243.947661-960303.sp%7CQ5ZJ66%7CSYEM_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:-1 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP55165%7CCRBB3_CHICK.for.1489541-1491034.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1489541-1491034.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1489541-1491034.sp%7CP55165%7CCRBB3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP55164%7CCRBA2_CHICK.for.1489517-1492661.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1489517-1492661.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1489517-1492661.sp%7CP55164%7CCRBA2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP10042%7CCRBA1_CHICK.for.1489538-1492658.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1489538-1492658.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1489538-1492658.sp%7CP10042%7CCRBA1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP49152%7CCRBA4_CHICK.for.1489541-1492658.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1489541-1492658.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1489541-1492658.sp%7CP49152%7CCRBA4_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28127%7CWNT4_MELGA.for.1553304-1554460.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553304-1554460.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553304-1554460.sp%7CP28127%7CWNT4_MELGA.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28128%7CWNT5A_MELGA.for.1553304-1554460.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553304-1554460.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553304-1554460.sp%7CP28128%7CWNT5A_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28129%7CWNT7A_MELGA.for.1553304-1554460.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553304-1554460.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553304-1554460.sp%7CP28129%7CWNT7A_MELGA.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ3L254%7CWNT7B_CHICK.for.1553241-1567801.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553241-1567801.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553241-1567801.sp%7CQ3L254%7CWNT7B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP49339%7CWNT11_CHICK.for.1553241-1567804.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553241-1567804.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553241-1567804.sp%7CP49339%7CWNT11_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ91029%7CWNT1_CHICK.for.1553262-1559667.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553262-1559667.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553262-1559667.sp%7CQ91029%7CWNT1_CHICK.p.exonerate
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28130%7CWNT7B_MELGA.for.1553304-1554460.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553304-1554460.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553304-1554460.sp%7CP28130%7CWNT7B_MELGA.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ98SN7%7CWNT2B_CHICK.for.1553229-1567783.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553229-1567783.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553229-1567783.sp%7CQ98SN7%7CWNT2B_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ2LMP1%7CWNT3A_CHICK.for.1553241-1567801.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553241-1567801.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553241-1567801.sp%7CQ2LMP1%7CWNT3A_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28125%7CWNT3A_MELGA.for.1553304-1554460.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553304-1554460.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553304-1554460.sp%7CP28125%7CWNT3A_MELGA.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28126%7CWNT3B_MELGA.for.1553304-1554460.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553304-1554460.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553304-1554460.sp%7CP28126%7CWNT3B_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP49337%7CWNT4_CHICK.for.1553259-1567825.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1553259-1567825.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1553259-1567825.sp%7CP49337%7CWNT4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28127%7CWNT4_MELGA.for.1583385-1584535.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583385-1584535.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583385-1584535.sp%7CP28127%7CWNT4_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28128%7CWNT5A_MELGA.for.1583385-1584535.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583385-1584535.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583385-1584535.sp%7CP28128%7CWNT5A_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28129%7CWNT7A_MELGA.for.1583385-1584535.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583385-1584535.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583385-1584535.sp%7CP28129%7CWNT7A_MELGA.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ3L254%7CWNT7B_CHICK.for.1583325-1585166.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583325-1585166.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583325-1585166.sp%7CQ3L254%7CWNT7B_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP49339%7CWNT11_CHICK.for.1583325-1585157.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583325-1585157.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583325-1585157.sp%7CP49339%7CWNT11_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ91029%7CWNT1_CHICK.for.1583349-1585157.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583349-1585157.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583349-1585157.sp%7CQ91029%7CWNT1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ98SN7%7CWNT2B_CHICK.for.1583316-1585157.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583316-1585157.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583316-1585157.sp%7CQ98SN7%7CWNT2B_CHICK.p.exonerate
#-------------------------------#
deleted:1 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CQ2LMP1%7CWNT3A_CHICK.for.1583325-1585379.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583325-1585379.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583325-1585379.sp%7CQ2LMP1%7CWNT3A_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28125%7CWNT3A_MELGA.for.1583385-1584535.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583385-1584535.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583385-1584535.sp%7CP28125%7CWNT3A_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP28126%7CWNT3B_MELGA.for.1583385-1584535.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583385-1584535.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583385-1584535.sp%7CP28126%7CWNT3B_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/12/sp%7CP49337%7CWNT4_CHICK.for.1583325-1585157.12.fasta -t /tmp/maker_6B3o0i/12/2284110.1583325-1585157.12.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/12/2284110.1583325-1585157.sp%7CP49337%7CWNT4_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:3 now processing 0
 ...processing 0 of 12
 ...processing 1 of 12
 ...processing 2 of 12
 ...processing 3 of 12
 ...processing 4 of 12
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 5 of 12
 ...processing 6 of 12
 ...processing 7 of 12
 ...processing 8 of 12
 ...processing 9 of 12
 ...processing 10 of 12
doing blastx of proteins
 ...processing 11 of 12
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
total clusters:3 now processing 0
 ...processing 0 of 11
 ...processing 1 of 11
 ...processing 2 of 11
 ...processing 3 of 11
 ...processing 4 of 11
 ...processing 5 of 11
 ...processing 6 of 11
 ...processing 7 of 11
 ...processing 8 of 11
 ...processing 9 of 11
 ...processing 10 of 11
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
 ...processing 0 of 9
 ...processing 1 of 9
 ...processing 2 of 9
 ...processing 3 of 9
 ...processing 4 of 9
 ...processing 5 of 9
 ...processing 6 of 9
 ...processing 7 of 9
 ...processing 8 of 9
total clusters:3 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing the chunk divide
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
preparing masked sequence
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
flattening protein clusters
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
prepare section files
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
processing all repeats
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
flattening protein clusters
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/0/2284509.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
running  blast search.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CP49702%7CARF5_CHICK.for.1383271-1385774.1.fasta -t /tmp/maker_6B3o0i/1/2284232.1383271-1385774.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.1383271-1385774.sp%7CP49702%7CARF5_CHICK.p.exonerate
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CP26990%7CARF6_CHICK.for.1384219-1385174.1.fasta -t /tmp/maker_6B3o0i/1/2284232.1384219-1385174.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.1384219-1385174.sp%7CP26990%7CARF6_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CQ5F3L1%7CKS6A5_CHICK.for.1002148-1003365.8.fasta -t /tmp/maker_6B3o0i/8/2284243.1002148-1003365.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284243.1002148-1003365.sp%7CQ5F3L1%7CKS6A5_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:29   current j:0
 j_size:29   current j:1
 j_size:29   current j:2
 j_size:29   current j:3
 j_size:29   current j:4
 j_size:29   current j:5
 j_size:29   current j:6
 j_size:29   current j:7
 j_size:29   current j:8
 j_size:29   current j:9
 j_size:29   current j:10
 j_size:29   current j:11
 j_size:29   current j:12
 j_size:29   current j:13
 j_size:29   current j:14
 j_size:29   current j:15
 j_size:29   current j:16
 j_size:29   current j:17
 j_size:29   current j:18
 j_size:29   current j:19
 j_size:29   current j:20
 j_size:29   current j:21
 j_size:29   current j:22
 j_size:29   current j:23
 j_size:29   current j:24
 j_size:29   current j:25
 j_size:29   current j:26
 j_size:29   current j:27
 j_size:29   current j:28
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
gathering ab-init output files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
flattening protein clusters
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
flattening protein clusters
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/0/2284341.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0 -pa 1
#-------------------------------#
flattening protein clusters
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1 -pa 1
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
re-running blast for edge cases...
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/1/blastprep/db.1388821-1420912.for_blastx.fasta
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.1388821-1420912.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.1388821.1420912.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.1388821.1420912.0.db%2E1388821-1420912%2Efor_blastx%2Efasta.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/21/sp%7CP0DJJ2%7CASTL_CHICK.for.851030-856872.21.fasta -t /tmp/maker_6B3o0i/21/2284471.851030-856872.21.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/21/2284471.851030-856872.sp%7CP0DJJ2%7CASTL_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
cleaning blastx...
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CQ5F3L4%7CDEN6A_CHICK.for.1437784-1447981.1.fasta -t /tmp/maker_6B3o0i/1/2284232.1437784-1447981.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.1437784-1447981.sp%7CQ5F3L4%7CDEN6A_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
prepare section files
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
prepare section files
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
merging blast reports...
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/0/2284471.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
flattening protein clusters
merging blast reports...
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
prepare section files
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
choosing best annotation set
running  blast search.
Choosing best annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/1/2283556.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 9
 ...processing 1 of 9
 ...processing 2 of 9
 ...processing 3 of 9
 ...processing 4 of 9
 ...processing 5 of 9
 ...processing 6 of 9
 ...processing 7 of 9
 ...processing 8 of 9
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/0/2284413.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
processing all repeats
prepare section files
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0 -pa 1
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284451.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/08/12/2284451//theVoid.2284451/1/2284451.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
prepare section files
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
flattening protein clusters
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
merging blast reports...
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
collecting blastx reports
deleted:0 hits
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CQ6U1I9%7CSGK1_CHICK.for.1341846-1342969.8.fasta -t /tmp/maker_6B3o0i/8/2284243.1341846-1342969.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284243.1341846-1342969.sp%7CQ6U1I9%7CSGK1_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
cleaning blastx...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
processing the chunk divide
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
collecting blastx repeatmasking
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
flattening protein clusters
Choosing best annotations
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:1 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing repeat masking
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 12
 ...processing 1 of 12
 ...processing 2 of 12
 ...processing 3 of 12
collecting blastx repeatmasking
 ...processing 4 of 12
 ...processing 5 of 12
 ...processing 6 of 12
 ...processing 7 of 12
 ...processing 8 of 12
 ...processing 9 of 12
 ...processing 10 of 12
 ...processing 11 of 12
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
deleted:0 hits
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 19 of 20
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/38/sp%7CQ1G7G9%7CTALD3_CHICK.for.327408-358039.38.fasta -t /tmp/maker_6B3o0i/38/2284484.327408-358039.38.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/38/2284484.327408-358039.sp%7CQ1G7G9%7CTALD3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
collecting blastx reports
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CQ90611%7CMMP2_CHICK.for.874743-875761.22.fasta -t /tmp/maker_6B3o0i/22/2284260.874743-875761.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.874743-875761.sp%7CQ90611%7CMMP2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZIV9%7CADSV_CHICK.for.1984259-1997382.41.fasta -t /tmp/maker_6B3o0i/41/2283556.1984259-1997382.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.1984259-1997382.sp%7CQ5ZIV9%7CADSV_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CP02640%7CVILI_CHICK.for.1984226-1997361.41.fasta -t /tmp/maker_6B3o0i/41/2283556.1984226-1997361.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.1984226-1997361.sp%7CP02640%7CVILI_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CO93510%7CGELS_CHICK.for.1984217-1998789.41.fasta -t /tmp/maker_6B3o0i/41/2283556.1984217-1998789.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.1984217-1998789.sp%7CO93510%7CGELS_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ90965%7CRAB2A_CHICK.for.2047783-2048741.41.fasta -t /tmp/maker_6B3o0i/41/2283556.2047783-2048741.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.2047783-2048741.sp%7CQ90965%7CRAB2A_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ1KME6%7CRAB6A_CHICK.for.2047738-2048741.41.fasta -t /tmp/maker_6B3o0i/41/2283556.2047738-2048741.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.2047738-2048741.sp%7CQ1KME6%7CRAB6A_CHICK.p.exonerate
#-------------------------------#
deleted:1 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5F470%7CRAB8A_CHICK.for.2047783-2048741.41.fasta -t /tmp/maker_6B3o0i/41/2283556.2047783-2048741.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.2047783-2048741.sp%7CQ5F470%7CRAB8A_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZIT5%7CRAB10_CHICK.for.2047783-2048741.41.fasta -t /tmp/maker_6B3o0i/41/2283556.2047783-2048741.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.2047783-2048741.sp%7CQ5ZIT5%7CRAB10_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZKU5%7CRAB14_CHICK.for.2047765-2052340.41.fasta -t /tmp/maker_6B3o0i/41/2283556.2047765-2052340.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.2047765-2052340.sp%7CQ5ZKU5%7CRAB14_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZLG1%7CRAB18_CHICK.for.2047738-2048741.41.fasta -t /tmp/maker_6B3o0i/41/2283556.2047738-2048741.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.2047738-2048741.sp%7CQ5ZLG1%7CRAB18_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284232.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/89/29/2284232//theVoid.2284232/1/2284232.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
choosing best annotation set
Choosing best annotations
merging blast reports...
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/1/sp%7CQ9YGI5%7CDNAS1_CHICK.for.1725700-1726733.1.fasta -t /tmp/maker_6B3o0i/1/2284232.1725700-1726733.1.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/1/2284232.1725700-1726733.sp%7CQ9YGI5%7CDNAS1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
processing chunk output
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
doing blastx of proteins
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:-1 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
doing blastx of proteins
 ...processing 2 of 3
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing the chunk divide
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx repeats
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
polishing proteins
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/24/sp%7CQ90751%7CBMP2_CHICK.for.530551-531707.24.fasta -t /tmp/maker_6B3o0i/24/2284284.530551-531707.24.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/24/2284284.530551-531707.sp%7CQ90751%7CBMP2_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/24/sp%7CP34822%7CDSL1_CHICK.for.530554-531707.24.fasta -t /tmp/maker_6B3o0i/24/2284284.530554-531707.24.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/24/2284284.530554-531707.sp%7CP34822%7CDSL1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/24/sp%7CQ9PVY0%7CRX1_CHICK.for.559003-560018.24.fasta -t /tmp/maker_6B3o0i/24/2284284.559003-560018.24.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/24/2284284.559003-560018.sp%7CQ9PVY0%7CRX1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing chunk output
flattening protein clusters
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/38/sp%7CQ1G7G9%7CTALD3_CHICK.for.386027-396245.38.fasta -t /tmp/maker_6B3o0i/38/2284484.386027-396245.38.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/38/2284484.386027-396245.sp%7CQ1G7G9%7CTALD3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/38/sp%7CQ5ZIR8%7CTIM9_CHICK.for.409070-412834.38.fasta -t /tmp/maker_6B3o0i/38/2284484.409070-412834.38.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/38/2284484.409070-412834.sp%7CQ5ZIR8%7CTIM9_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/0/2284260.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
merging blast reports...
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
total clusters:2 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
in cluster::shadow_cluster...
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
merging blast reports...
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CQ90611%7CMMP2_CHICK.for.921251-922236.22.fasta -t /tmp/maker_6B3o0i/22/2284260.921251-922236.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.921251-922236.sp%7CQ90611%7CMMP2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CQ90611%7CMMP2_CHICK.for.956986-957977.22.fasta -t /tmp/maker_6B3o0i/22/2284260.956986-957977.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.956986-957977.sp%7CQ90611%7CMMP2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 11
 ...processing 1 of 11
 ...processing 2 of 11
 ...processing 3 of 11
 ...processing 4 of 11
 ...processing 5 of 11
 ...processing 6 of 11
 ...processing 7 of 11
 ...processing 8 of 11
 ...processing 9 of 11
 ...processing 10 of 11
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
flattening protein clusters
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
examining contents of the fasta file and run log
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing masked sequence
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits



--Next Contig--

preparing ab-inits
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284673
Length: 4490141
#---------------------------------------------------------------------


deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
deleted:0 hits
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:-11 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:-12 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
deleted:-11 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
deleted:-5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
deleted:0 hits
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:-5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CQ90611%7CMMP2_CHICK.for.1019442-1020448.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1019442-1020448.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1019442-1020448.sp%7CQ90611%7CMMP2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
polishing proteins
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/11/sp%7CQ90835%7CEF1A_CHICK.for.1241560-1246088.11.fasta -t /tmp/maker_6B3o0i/11/2284413.1241560-1246088.11.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/11/2284413.1241560-1246088.sp%7CQ90835%7CEF1A_CHICK.p.exonerate
#-------------------------------#
flattening protein clusters
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-10 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284243.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/06/FE/2284243//theVoid.2284243/1/2284243.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:-7 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:-10 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CQ92010%7CZBT14_CHICK.for.1703548-1705122.8.fasta -t /tmp/maker_6B3o0i/8/2284243.1703548-1705122.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284243.1703548-1705122.sp%7CQ92010%7CZBT14_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:-9 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CO73691%7CEGR1_CHICK.for.1703542-1704518.8.fasta -t /tmp/maker_6B3o0i/8/2284243.1703542-1704518.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284243.1703542-1704518.sp%7CO73691%7CEGR1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CO73693%7CEGR1_TAEGU.for.1703542-1704518.8.fasta -t /tmp/maker_6B3o0i/8/2284243.1703542-1704518.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284243.1703542-1704518.sp%7CO73693%7CEGR1_TAEGU.p.exonerate
#-------------------------------#
merging blast reports...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CQ5F4B1%7CPGP_CHICK.for.1715822-1716945.8.fasta -t /tmp/maker_6B3o0i/8/2284243.1715822-1716945.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284243.1715822-1716945.sp%7CQ5F4B1%7CPGP_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:-11 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
collecting blastx reports
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9YH13%7CHXC8_CHICK.for.7576-8582.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7576-8582.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7576-8582.sp%7CQ9YH13%7CHXC8_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ90VZ9%7CHXA7_CHICK.for.7576-8591.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7576-8591.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7576-8591.sp%7CQ90VZ9%7CHXA7_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ98924%7CHXA9_CHICK.for.5675-8594.37.fasta -t /tmp/maker_6B3o0i/37/2284450.5675-8594.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.5675-8594.sp%7CQ98924%7CHXA9_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
processing the chunk divide
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP13544%7CHXD1_CHICK.for.7606-8591.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7606-8591.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7606-8591.sp%7CP13544%7CHXD1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23459%7CHXD8_CHICK.for.7585-8573.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7585-8573.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7585-8573.sp%7CP23459%7CHXD8_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9W6D8%7CBARX1_CHICK.for.7585-8570.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7585-8570.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7585-8570.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9YH13%7CHXC8_CHICK.for.23481-24475.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23481-24475.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23481-24475.sp%7CQ9YH13%7CHXC8_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5YLH5%7CHXA6_CHICK.for.23478-40901.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23478-40901.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23478-40901.sp%7CQ5YLH5%7CHXA6_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP19601%7CSAX1_CHICK.for.39919-40895.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39919-40895.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39919-40895.sp%7CP19601%7CSAX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ90VZ9%7CHXA7_CHICK.for.39907-40922.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39907-40922.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39907-40922.sp%7CQ90VZ9%7CHXA7_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ98924%7CHXA9_CHICK.for.39919-40898.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39919-40898.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39919-40898.sp%7CQ98924%7CHXA9_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP13544%7CHXD1_CHICK.for.23499-24472.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23499-24472.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23499-24472.sp%7CP13544%7CHXD1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ91975%7CDBX2_CHICK.for.23499-24475.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23499-24475.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23499-24475.sp%7CQ91975%7CDBX2_CHICK.p.exonerate
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14840%7CHXB4_CHICK.for.23475-24469.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23475-24469.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23475-24469.sp%7CP14840%7CHXB4_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14838%7CHXB5_CHICK.for.39898-40943.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39898-40943.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39898-40943.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
deleted:2 hits
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14839%7CHXB6_CHICK.for.23478-24517.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23478-24517.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23478-24517.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP28362%7CMSX2_CHICK.for.39919-40922.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39919-40922.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39919-40922.sp%7CP28362%7CMSX2_CHICK.p.exonerate
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9W6D8%7CBARX1_CHICK.for.23490-24460.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23490-24460.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23490-24460.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP47237%7CPAX6_CHICK.for.39919-40904.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39919-40904.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39919-40904.sp%7CP47237%7CPAX6_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5YLH5%7CHXA6_CHICK.for.56103-57130.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56103-57130.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56103-57130.sp%7CQ5YLH5%7CHXA6_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24342%7CHXD11_CHICK.for.56043-57085.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56043-57085.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56043-57085.sp%7CP24342%7CHXD11_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ02814%7CHMD2_CHICK.for.56124-57085.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56124-57085.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56124-57085.sp%7CQ02814%7CHMD2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14840%7CHXB4_CHICK.for.56073-57115.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56073-57115.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56073-57115.sp%7CP14840%7CHXB4_CHICK.p.exonerate
#-------------------------------#
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
merging blast reports...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24340%7CHXD9_CHICK.for.56115-57085.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56115-57085.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56115-57085.sp%7CP24340%7CHXD9_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP15142%7CHM7X_CHICK.for.7585-8570.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7585-8570.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7585-8570.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24342%7CHXD11_CHICK.for.7528-8582.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7528-8582.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7528-8582.sp%7CP24342%7CHXD11_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP46692%7CHMD1_CHICK.for.7588-8576.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7588-8576.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7588-8576.sp%7CP46692%7CHMD1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ90X25%7CHXA13_CHICK.for.7513-8570.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7513-8570.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7513-8570.sp%7CQ90X25%7CHXA13_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP28361%7CMSX1_CHICK.for.7588-8576.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7588-8576.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7588-8576.sp%7CP28361%7CMSX1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23681%7CHXB8_CHICK.for.7576-8501.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7576-8501.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7576-8501.sp%7CP23681%7CHXB8_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9YH13%7CHXC8_CHICK.for.39910-40919.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39910-40919.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39910-40919.sp%7CQ9YH13%7CHXC8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24341%7CHXD10_CHICK.for.23451-24472.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23451-24472.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23451-24472.sp%7CP24341%7CHXD10_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9PVY0%7CRX1_CHICK.for.23490-24484.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23490-24484.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23490-24484.sp%7CQ9PVY0%7CRX1_CHICK.p.exonerate
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9DED6%7CBAX1B_CHICK.for.39904-40889.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39904-40889.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39904-40889.sp%7CQ9DED6%7CBAX1B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24343%7CHXD12_CHICK.for.23412-24460.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23412-24460.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23412-24460.sp%7CP24343%7CHXD12_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP13544%7CHXD1_CHICK.for.39928-40889.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39928-40889.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39928-40889.sp%7CP13544%7CHXD1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ91975%7CDBX2_CHICK.for.39928-40886.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39928-40886.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39928-40886.sp%7CQ91975%7CDBX2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14840%7CHXB4_CHICK.for.39895-40904.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39895-40904.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39895-40904.sp%7CP14840%7CHXB4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23459%7CHXD8_CHICK.for.23412-24475.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23412-24475.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23412-24475.sp%7CP23459%7CHXD8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14839%7CHXB6_CHICK.for.39907-40925.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39907-40925.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39907-40925.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17277%7CHXA4_CHICK.for.23475-24508.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23475-24508.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23475-24508.sp%7CP17277%7CHXA4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9W6D8%7CBARX1_CHICK.for.39916-40889.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39916-40889.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39916-40889.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ6B3N0%7CHXA5_CHICK.for.56073-57130.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56073-57130.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56073-57130.sp%7CQ6B3N0%7CHXA5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24341%7CHXD10_CHICK.for.56115-57085.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56115-57085.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56115-57085.sp%7CP24341%7CHXD10_CHICK.p.exonerate
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP79775%7CANF1_CHICK.for.56115-57094.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56115-57094.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56115-57094.sp%7CP79775%7CANF1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP13544%7CHXD1_CHICK.for.56124-57085.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56124-57085.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56124-57085.sp%7CP13544%7CHXD1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14838%7CHXB5_CHICK.for.56094-57130.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56094-57130.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56094-57130.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17277%7CHXA4_CHICK.for.56013-57211.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56013-57211.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56013-57211.sp%7CP17277%7CHXA4_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5YLH5%7CHXA6_CHICK.for.7534-8576.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7534-8576.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7534-8576.sp%7CQ5YLH5%7CHXA6_CHICK.p.exonerate
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9DED6%7CBAX1B_CHICK.for.7585-8570.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7585-8570.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7585-8570.sp%7CQ9DED6%7CBAX1B_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP31259%7CHXB1_CHICK.for.7615-8702.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7615-8702.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7615-8702.sp%7CP31259%7CHXB1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17278%7CHXD4_CHICK.for.7597-8576.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7597-8576.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7597-8576.sp%7CP17278%7CHXD4_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14839%7CHXB6_CHICK.for.7594-8576.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7594-8576.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7594-8576.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ6B3N0%7CHXA5_CHICK.for.23472-24493.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23472-24493.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23472-24493.sp%7CQ6B3N0%7CHXA5_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP15142%7CHM7X_CHICK.for.23475-24460.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23475-24460.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23475-24460.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24341%7CHXD10_CHICK.for.39901-40913.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39901-40913.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39901-40913.sp%7CP24341%7CHXD10_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9PVY0%7CRX1_CHICK.for.39919-40916.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39919-40916.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39919-40916.sp%7CQ9PVY0%7CRX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP79775%7CANF1_CHICK.for.39916-40898.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39916-40898.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39916-40898.sp%7CP79775%7CANF1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ02814%7CHMD2_CHICK.for.23499-24460.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23499-24460.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23499-24460.sp%7CQ02814%7CHMD2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ90X25%7CHXA13_CHICK.for.39886-40913.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39886-40913.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39886-40913.sp%7CQ90X25%7CHXA13_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17278%7CHXD4_CHICK.for.23475-24469.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23475-24469.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23475-24469.sp%7CP17278%7CHXD4_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP50577%7CDLX5_CHICK.for.23499-24517.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23499-24517.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23499-24517.sp%7CP50577%7CDLX5_CHICK.p.exonerate
#-------------------------------#
collecting blastx repeatmasking
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23459%7CHXD8_CHICK.for.39904-40895.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39904-40895.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39904-40895.sp%7CP23459%7CHXD8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24340%7CHXD9_CHICK.for.23490-24460.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23490-24460.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23490-24460.sp%7CP24340%7CHXD9_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17277%7CHXA4_CHICK.for.39856-40916.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39856-40916.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39856-40916.sp%7CP17277%7CHXA4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23681%7CHXB8_CHICK.for.23475-24391.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23475-24391.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23475-24391.sp%7CP23681%7CHXB8_CHICK.p.exonerate
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9YH13%7CHXC8_CHICK.for.56115-57109.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56115-57109.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56115-57109.sp%7CQ9YH13%7CHXC8_CHICK.p.exonerate
#-------------------------------#
collecting blastx reports
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP19601%7CSAX1_CHICK.for.56106-57091.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56106-57091.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56106-57091.sp%7CP19601%7CSAX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ98924%7CHXA9_CHICK.for.56115-57094.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56115-57094.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56115-57094.sp%7CQ98924%7CHXA9_CHICK.p.exonerate
#-------------------------------#
deleted:1 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ91975%7CDBX2_CHICK.for.56124-57082.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56124-57082.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56124-57082.sp%7CQ91975%7CDBX2_CHICK.p.exonerate
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23459%7CHXD8_CHICK.for.56115-57160.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56115-57160.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56115-57160.sp%7CP23459%7CHXD8_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9W6D8%7CBARX1_CHICK.for.56115-57085.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56115-57085.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56115-57085.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24341%7CHXD10_CHICK.for.7558-8579.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7558-8579.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7558-8579.sp%7CP24341%7CHXD10_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP79775%7CANF1_CHICK.for.7597-8579.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7597-8579.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7597-8579.sp%7CP79775%7CANF1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ02814%7CHMD2_CHICK.for.7600-8570.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7600-8570.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7600-8570.sp%7CQ02814%7CHMD2_CHICK.p.exonerate
#-------------------------------#
collecting blastx repeatmasking
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14838%7CHXB5_CHICK.for.7597-8576.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7597-8576.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7597-8576.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24340%7CHXD9_CHICK.for.7594-8573.37.fasta -t /tmp/maker_6B3o0i/37/2284450.7594-8573.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.7594-8573.sp%7CP24340%7CHXD9_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ6B3N0%7CHXA5_CHICK.for.34717-40943.37.fasta -t /tmp/maker_6B3o0i/37/2284450.34717-40943.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.34717-40943.sp%7CQ6B3N0%7CHXA5_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP15142%7CHM7X_CHICK.for.39892-40889.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39892-40889.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39892-40889.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP19601%7CSAX1_CHICK.for.23490-24466.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23490-24466.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23490-24466.sp%7CP19601%7CSAX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ90VZ9%7CHXA7_CHICK.for.22293-24523.37.fasta -t /tmp/maker_6B3o0i/37/2284450.22293-24523.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.22293-24523.sp%7CQ90VZ9%7CHXA7_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ98924%7CHXA9_CHICK.for.23499-24472.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23499-24472.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23499-24472.sp%7CQ98924%7CHXA9_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ02814%7CHMD2_CHICK.for.39928-40889.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39928-40889.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39928-40889.sp%7CQ02814%7CHMD2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CO93367%7CTLX3_CHICK.for.23430-24475.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23430-24475.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23430-24475.sp%7CO93367%7CTLX3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17278%7CHXD4_CHICK.for.39856-40943.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39856-40943.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39856-40943.sp%7CP17278%7CHXD4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14838%7CHXB5_CHICK.for.23472-24499.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23472-24499.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23472-24499.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP28361%7CMSX1_CHICK.for.39919-40922.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39919-40922.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39919-40922.sp%7CP28361%7CMSX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24340%7CHXD9_CHICK.for.39919-40889.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39919-40889.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39919-40889.sp%7CP24340%7CHXD9_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9PVN2%7CVAX1_CHICK.for.23490-24541.37.fasta -t /tmp/maker_6B3o0i/37/2284450.23490-24541.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.23490-24541.sp%7CQ9PVN2%7CVAX1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23681%7CHXB8_CHICK.for.39919-40820.37.fasta -t /tmp/maker_6B3o0i/37/2284450.39919-40820.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.39919-40820.sp%7CP23681%7CHXB8_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP15142%7CHM7X_CHICK.for.56091-57085.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56091-57085.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56091-57085.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ90VZ9%7CHXA7_CHICK.for.56100-57148.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56100-57148.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56100-57148.sp%7CQ90VZ9%7CHXA7_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP31259%7CHXB1_CHICK.for.56106-57133.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56106-57133.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56106-57133.sp%7CP31259%7CHXB1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17278%7CHXD4_CHICK.for.56073-57133.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56073-57133.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56073-57133.sp%7CP17278%7CHXD4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14839%7CHXB6_CHICK.for.56106-57127.37.fasta -t /tmp/maker_6B3o0i/37/2284450.56106-57127.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.56106-57127.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx of proteins
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ8QFV0%7CKCNT1_CHICK.for.2345159-2373363.41.fasta -t /tmp/maker_6B3o0i/41/2283556.2345159-2373363.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.2345159-2373363.sp%7CQ8QFV0%7CKCNT1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
cleaning blastx...
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
collecting blastx reports
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:1 hits
collecting blastx reports
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
merging blast reports...
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CQ90611%7CMMP2_CHICK.for.1106058-1107061.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1106058-1107061.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1106058-1107061.sp%7CQ90611%7CMMP2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/10/sp%7CP17153%7CANXA5_CHICK.for.1540929-1547820.10.fasta -t /tmp/maker_6B3o0i/10/2284341.1540929-1547820.10.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/10/2284341.1540929-1547820.sp%7CP17153%7CANXA5_CHICK.p.exonerate
#-------------------------------#
prepare section files
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
choosing best annotation set
Making transcripts
Choosing best annotations
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CO93436%7CSTAM2_CHICK.for.1161291-1171852.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1161291-1171852.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1161291-1171852.sp%7CO93436%7CSTAM2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
cleaning blastx...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1 -pa 1
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
merging blast reports...
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2 -pa 1
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
deleted:0 hits
prepare section files
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2283556.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/3E/C5/2283556//theVoid.2283556/2/2283556.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
re-running blast for edge cases...
doing blastx of proteins
preparing evidence clusters for annotations
running  blast search.
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/37/blastprep/db.73149-111331.for_blastx.fasta
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.73149-111331.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.73149.111331.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.73149.111331.0.db%2E73149-111331%2Efor_blastx%2Efasta.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284341.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2E/E5/2284341//theVoid.2284341/1/2284341.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:13 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
choosing best annotation set
Choosing best annotations
doing repeat masking
collecting blastx reports
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/41/sp%7CQ5ZJI9%7CUBAC1_CHICK.for.2461824-2481467.41.fasta -t /tmp/maker_6B3o0i/41/2283556.2461824-2481467.41.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/41/2283556.2461824-2481467.sp%7CQ5ZJI9%7CUBAC1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 0 of 2
 ...processing 1 of 2
cleaning blastx...
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
running  blast search.
clustering transcripts into genes for annotations
doing blastx repeats
Processing transcripts into genes
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
flattening protein clusters
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP79775%7CANF1_CHICK.for.84728-94650.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-94650.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-94650.sp%7CP79775%7CANF1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CO93353%7CHXA3_CHICK.for.82749-101686.37.fasta -t /tmp/maker_6B3o0i/37/2284450.82749-101686.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.82749-101686.sp%7CO93353%7CHXA3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ08727%7CHXA2_CHICK.for.84713-101668.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84713-101668.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84713-101668.sp%7CQ08727%7CHXA2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23682%7CHXB3_CHICK.for.82749-101677.37.fasta -t /tmp/maker_6B3o0i/37/2284450.82749-101677.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.82749-101677.sp%7CP23682%7CHXB3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP31259%7CHXB1_CHICK.for.84737-101731.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84737-101731.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84737-101731.sp%7CP31259%7CHXB1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14838%7CHXB5_CHICK.for.84728-101701.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101701.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101701.sp%7CP14838%7CHXB5_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ6B3N0%7CHXA5_CHICK.for.84728-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101674.sp%7CQ6B3N0%7CHXA5_CHICK.p.exonerate
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
processing the chunk divide
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/0/2284284.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17278%7CHXD4_CHICK.for.84728-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101674.sp%7CP17278%7CHXD4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14840%7CHXB4_CHICK.for.84728-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101674.sp%7CP14840%7CHXB4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP17277%7CHXA4_CHICK.for.84728-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101674.sp%7CP17277%7CHXA4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5YLH5%7CHXA6_CHICK.for.84686-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84686-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84686-101674.sp%7CQ5YLH5%7CHXA6_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP13544%7CHXD1_CHICK.for.84737-101677.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84737-101677.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84737-101677.sp%7CP13544%7CHXD1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ90VZ9%7CHXA7_CHICK.for.84728-101677.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101677.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101677.sp%7CQ90VZ9%7CHXA7_CHICK.p.exonerate
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
choosing best annotation set
Choosing best annotations
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP14839%7CHXB6_CHICK.for.84725-101731.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84725-101731.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84725-101731.sp%7CP14839%7CHXB6_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ98924%7CHXA9_CHICK.for.84722-101677.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84722-101677.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84722-101677.sp%7CQ98924%7CHXA9_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24340%7CHXD9_CHICK.for.84725-101665.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84725-101665.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84725-101665.sp%7CP24340%7CHXD9_CHICK.p.exonerate
#-------------------------------#
flattening protein clusters
merging blast reports...
merging blast reports...
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP15142%7CHM7X_CHICK.for.84692-101665.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84692-101665.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84692-101665.sp%7CP15142%7CHM7X_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24341%7CHXD10_CHICK.for.84722-101680.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84722-101680.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84722-101680.sp%7CP24341%7CHXD10_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP23459%7CHXD8_CHICK.for.84641-101695.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84641-101695.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84641-101695.sp%7CP23459%7CHXD8_CHICK.p.exonerate
#-------------------------------#
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP24342%7CHXD11_CHICK.for.84686-101683.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84686-101683.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84686-101683.sp%7CP24342%7CHXD11_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9YH13%7CHXC8_CHICK.for.84710-101689.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84710-101689.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84710-101689.sp%7CQ9YH13%7CHXC8_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing the chunk divide
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9DEB6%7CCDX1_CHICK.for.84701-101683.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84701-101683.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84701-101683.sp%7CQ9DEB6%7CCDX1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP46692%7CHMD1_CHICK.for.84701-101683.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84701-101683.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84701-101683.sp%7CP46692%7CHMD1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ6RFL5%7CBSH_CHICK.for.84728-101668.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101668.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101668.sp%7CQ6RFL5%7CBSH_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ05917%7CHME2_CHICK.for.84728-101665.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101665.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101665.sp%7CQ05917%7CHME2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP19601%7CSAX1_CHICK.for.84719-101665.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84719-101665.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84719-101665.sp%7CP19601%7CSAX1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9W6D8%7CBARX1_CHICK.for.84692-101713.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84692-101713.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84692-101713.sp%7CQ9W6D8%7CBARX1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9DED6%7CBAX1B_CHICK.for.84728-101713.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101713.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101713.sp%7CQ9DED6%7CBAX1B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ02814%7CHMD2_CHICK.for.84728-101665.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101665.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101665.sp%7CQ02814%7CHMD2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP28362%7CMSX2_CHICK.for.84722-101713.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84722-101713.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84722-101713.sp%7CP28362%7CMSX2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP50577%7CDLX5_CHICK.for.84728-101716.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101716.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101716.sp%7CP50577%7CDLX5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CO93385%7CPITX2_CHICK.for.84692-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84692-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84692-101674.sp%7CO93385%7CPITX2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ05502%7CHHEX_CHICK.for.84728-101677.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101677.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101677.sp%7CQ05502%7CHHEX_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ05916%7CHME1_CHICK.for.84737-101665.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84737-101665.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84737-101665.sp%7CQ05916%7CHME1_CHICK.p.exonerate
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP28361%7CMSX1_CHICK.for.84722-101665.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84722-101665.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84722-101665.sp%7CP28361%7CMSX1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP56673%7CPITX1_CHICK.for.84689-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84689-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84689-101674.sp%7CP56673%7CPITX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9PVX0%7CRX2_CHICK.for.84728-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101674.sp%7CQ9PVX0%7CRX2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ9PVY0%7CRX1_CHICK.for.84728-101674.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84728-101674.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84728-101674.sp%7CQ9PVY0%7CRX1_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
prepare section files
deleted:0 hits
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ91975%7CDBX2_CHICK.for.84737-101683.37.fasta -t /tmp/maker_6B3o0i/37/2284450.84737-101683.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.84737-101683.sp%7CQ91975%7CDBX2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 11
 ...processing 1 of 11
doing blastx of proteins
 ...processing 2 of 11
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
 ...processing 3 of 11
 ...processing 4 of 11
 ...processing 5 of 11
doing blastx of proteins
 ...processing 6 of 11
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
 ...processing 7 of 11
 ...processing 8 of 11
clustering transcripts into genes for annotations
Processing transcripts into genes
 ...processing 9 of 11
 ...processing 10 of 11
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 9
 ...processing 1 of 9
 ...processing 2 of 9
 ...processing 3 of 9
 ...processing 4 of 9
 ...processing 5 of 9
 ...processing 6 of 9
 ...processing 7 of 9
 ...processing 8 of 9
total clusters:3 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
total clusters:3 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
choosing best annotation set
Choosing best annotations
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CP02542%7CDESM_CHICK.for.1334889-1342362.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1334889-1342362.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1334889-1342362.sp%7CP02542%7CDESM_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CP13648%7CLMNA_CHICK.for.1334889-1342314.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1334889-1342314.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1334889-1342314.sp%7CP13648%7CLMNA_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CO93532%7CK2CO_CHICK.for.1334889-1342506.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1334889-1342506.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1334889-1342506.sp%7CO93532%7CK2CO_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CP14732%7CLMNB2_CHICK.for.1334883-1342323.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1334883-1342323.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1334883-1342323.sp%7CP14732%7CLMNB2_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CP09654%7CVIME_CHICK.for.1334226-1342581.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1334226-1342581.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1334226-1342581.sp%7CP09654%7CVIME_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CP16053%7CNFM_CHICK.for.1334829-1342572.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1334829-1342572.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1334829-1342572.sp%7CP16053%7CNFM_CHICK.p.exonerate
#-------------------------------#
deleted:1 hits
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
adding statistics to annotations
Calculating annotation quality statistics
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing chunk output
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
processing chunk output
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
deleted:0 hits
clustering transcripts into genes for annotations
processing chunk output
doing blastx of proteins
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
merging blast reports...
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
processing contig output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/21/sp%7CQ9PVY0%7CRX1_CHICK.for.1655462-1656447.21.fasta -t /tmp/maker_6B3o0i/21/2284471.1655462-1656447.21.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/21/2284471.1655462-1656447.sp%7CQ9PVY0%7CRX1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/21/sp%7CQ90963%7CPRRX2_CHICK.for.1655519-1656486.21.fasta -t /tmp/maker_6B3o0i/21/2284471.1655519-1656486.21.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/21/2284471.1655519-1656486.sp%7CQ90963%7CPRRX2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/21/sp%7CO73592%7CMIXL1_CHICK.for.1655483-1656444.21.fasta -t /tmp/maker_6B3o0i/21/2284471.1655483-1656444.21.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/21/2284471.1655483-1656444.sp%7CO73592%7CMIXL1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing masked sequence
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
examining contents of the fasta file and run log
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
prepare section files
doing repeat masking
preparing evidence clusters for annotations
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters



--Next Contig--

collecting blastx reports
processing chunk output
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284676
Length: 1527740
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
collecting blastx repeatmasking
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
flattening protein clusters
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
gathering ab-init output files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/0/2284484.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
choosing best annotation set
Choosing best annotations
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing chunk output
processing chunk output
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:1 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
preparing evidence clusters for annotations
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/0/2284289.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
prepare section files
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
examining contents of the fasta file and run log
flattening protein clusters



--Next Contig--

doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284688
Length: 3850273
#---------------------------------------------------------------------


doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2 -pa 1
#-------------------------------#
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
choosing best annotation set
Choosing best annotations
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
flattening protein clusters
deleted:0 hits
prepare section files
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
collecting blastx repeatmasking
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
choosing best annotation set
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Choosing best annotations
processing all repeats
doing blastx of proteins
running  blast search.
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:31   current j:0
 j_size:31   current j:1
 j_size:31   current j:2
 j_size:31   current j:3
 j_size:31   current j:4
 j_size:31   current j:5
 j_size:31   current j:6
 j_size:31   current j:7
 j_size:31   current j:8
 j_size:31   current j:9
 j_size:31   current j:10
 j_size:31   current j:11
 j_size:31   current j:12
 j_size:31   current j:13
 j_size:31   current j:14
 j_size:31   current j:15
 j_size:31   current j:16
 j_size:31   current j:17
 j_size:31   current j:18
 j_size:31   current j:19
 j_size:31   current j:20
 j_size:31   current j:21
 j_size:31   current j:22
 j_size:31   current j:23
 j_size:31   current j:24
 j_size:31   current j:25
 j_size:31   current j:26
 j_size:31   current j:27
 j_size:31   current j:28
 j_size:31   current j:29
 j_size:31   current j:30
...finished clustering.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx of proteins
running  blast search.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CQ9DER7%7CTLL1_CHICK.for.1501219-1510956.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1501219-1510956.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1501219-1510956.sp%7CQ9DER7%7CTLL1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/22/sp%7CQ9DER7%7CTLL1_CHICK.for.1536511-1560186.22.fasta -t /tmp/maker_6B3o0i/22/2284260.1536511-1560186.22.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/22/2284260.1536511-1560186.sp%7CQ9DER7%7CTLL1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
cleaning blastx...
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284471.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C4/F0/2284471//theVoid.2284471/1/2284471.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
collecting blastx reports
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
clustering transcripts into genes for annotations
Processing transcripts into genes
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/24/sp%7CP79996%7CMK09_CHICK.for.1174817-1193436.24.fasta -t /tmp/maker_6B3o0i/24/2284284.1174817-1193436.24.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/24/2284284.1174817-1193436.sp%7CP79996%7CMK09_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
collecting blastx repeatmasking
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing the chunk divide
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
processing contig output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
doing blastx of proteins



--Next Contig--

deleted:0 hits
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284700
Length: 1770685
#---------------------------------------------------------------------


deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0 -pa 1
#-------------------------------#
deleted:0 hits
setting up GFF3 output and fasta chunks
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
clustering transcripts into genes for annotations
Processing transcripts into genes
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0 -pa 1
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
merging blast reports...
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
deleted:0 hits
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
processing chunk output
doing blastx repeats
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
merging blast reports...
collecting blastx reports
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:3 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
choosing best annotation set
Choosing best annotations
flattening protein clusters
processing chunk output
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
preparing evidence clusters for annotations
running  blast search.
flattening protein clusters
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284484.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/99/AC/2284484//theVoid.2284484/1/2284484.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:35   current j:0
 j_size:35   current j:1
 j_size:35   current j:2
 j_size:35   current j:3
 j_size:35   current j:4
 j_size:35   current j:5
 j_size:35   current j:6
 j_size:35   current j:7
 j_size:35   current j:8
 j_size:35   current j:9
 j_size:35   current j:10
 j_size:35   current j:11
 j_size:35   current j:12
 j_size:35   current j:13
 j_size:35   current j:14
 j_size:35   current j:15
 j_size:35   current j:16
 j_size:35   current j:17
 j_size:35   current j:18
 j_size:35   current j:19
 j_size:35   current j:20
 j_size:35   current j:21
 j_size:35   current j:22
 j_size:35   current j:23
 j_size:35   current j:24
 j_size:35   current j:25
 j_size:35   current j:26
 j_size:35   current j:27
 j_size:35   current j:28
 j_size:35   current j:29
 j_size:35   current j:30
 j_size:35   current j:31
 j_size:35   current j:32
 j_size:35   current j:33
 j_size:35   current j:34
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
processing the chunk divide
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
preparing masked sequence
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing ab-inits
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284413.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/58/7E/2284413//theVoid.2284413/1/2284413.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2 -pa 1
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
collecting blastx reports
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
merging blast reports...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing the chunk divide
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
polishing proteins
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx reports
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZMA3%7CRBM24_CHICK.for.641997-642985.37.fasta -t /tmp/maker_6B3o0i/37/2284450.641997-642985.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.641997-642985.sp%7CQ5ZMA3%7CRBM24_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZJX4%7CRBM38_CHICK.for.641997-642985.37.fasta -t /tmp/maker_6B3o0i/37/2284450.641997-642985.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.641997-642985.sp%7CQ5ZJX4%7CRBM38_CHICK.p.exonerate
#-------------------------------#
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZI72%7CHNRDL_CHICK.for.640295-642979.37.fasta -t /tmp/maker_6B3o0i/37/2284450.640295-642979.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.640295-642979.sp%7CQ5ZI72%7CHNRDL_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZL67%7CNF2L1_CHICK.for.655179-656729.37.fasta -t /tmp/maker_6B3o0i/37/2284450.655179-656729.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.655179-656729.sp%7CQ5ZL67%7CNF2L1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
cleaning blastx...
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
examining contents of the fasta file and run log
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:2 hits
clustering transcripts into genes for annotations
Processing transcripts into genes



--Next Contig--

choosing best annotation set
Choosing best annotations
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284707
Length: 1392902
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ5F415%7CTBC23_CHICK.for.57029-70101.31.fasta -t /tmp/maker_6B3o0i/31/2284498.57029-70101.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.57029-70101.sp%7CQ5F415%7CTBC23_CHICK.p.exonerate
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
cleaning blastx...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing chunk output
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
doing blastx of proteins
running  blast search.
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
merging blast reports...
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
choosing best annotation set
doing blastx repeats
Choosing best annotations
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing chunk output
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/24/sp%7CQ90751%7CBMP2_CHICK.for.1518599-1528477.24.fasta -t /tmp/maker_6B3o0i/24/2284284.1518599-1528477.24.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/24/2284284.1518599-1528477.sp%7CQ90751%7CBMP2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/24/sp%7CQ90752%7CBMP4_CHICK.for.1518599-1528477.24.fasta -t /tmp/maker_6B3o0i/24/2284284.1518599-1528477.24.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/24/2284284.1518599-1528477.sp%7CQ90752%7CBMP4_CHICK.p.exonerate
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/24/sp%7CP34822%7CDSL1_CHICK.for.1524601-1528477.24.fasta -t /tmp/maker_6B3o0i/24/2284284.1524601-1528477.24.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/24/2284284.1524601-1528477.sp%7CP34822%7CDSL1_CHICK.p.exonerate
deleted:0 hits
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing repeat masking
collecting blastx repeatmasking
processing chunk output
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ5F415%7CTBC23_CHICK.for.82219-95440.31.fasta -t /tmp/maker_6B3o0i/31/2284498.82219-95440.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.82219-95440.sp%7CQ5F415%7CTBC23_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
choosing best annotation set
Choosing best annotations
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/1/2284260.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx repeatmasking
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
preparing evidence clusters for annotations
preparing evidence clusters for annotations
flattening protein clusters
Preparing evidence for hint based annotation
Preparing evidence for hint based annotation
deleted:0 hits
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
collecting blastx reports
deleted:1 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
 ...processing 4 of 5
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
deleted:5 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
preparing evidence clusters for annotations
running  blast search.
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284260.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CC/3F/2284260//theVoid.2284260/2/2284260.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:4 hits
deleted:0 hits
deleted:3 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
processing chunk output
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx repeatmasking
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:3 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/0/2284450.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
flattening protein clusters
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
collecting blastx reports
choosing best annotation set
Choosing best annotations
merging blast reports...
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing the chunk divide
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
preparing evidence clusters for annotations
running  blast search.
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/0/2284552.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing contig output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
examining contents of the fasta file and run log
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#



--Next Contig--

doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284717
Length: 3205279
#---------------------------------------------------------------------


deleted:0 hits
setting up GFF3 output and fasta chunks
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:2 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
doing blastx repeats
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing contig output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
annotating transcripts
Making transcripts
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
collecting blastx reports
deleted:2 hits
processing chunk output
doing blastx of proteins
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

processing chunk output
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284722
Length: 1759360
#---------------------------------------------------------------------


merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ5F362%7CCC50A_CHICK.for.429471-436162.31.fasta -t /tmp/maker_6B3o0i/31/2284498.429471-436162.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.429471-436162.sp%7CQ5F362%7CCC50A_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
examining contents of the fasta file and run log
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284726
Length: 3125981
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1 -pa 1
#-------------------------------#
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
gathering ab-init output files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
preparing evidence clusters for annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
processing all repeats
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
preparing evidence clusters for annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing masked sequence
deleted:0 hits
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
flattening protein clusters
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
gathering ab-init output files
collecting blastx reports
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284284.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CD/98/2284284//theVoid.2284284/1/2284284.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing evidence clusters for annotations
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/24/sp%7CP32046%7CRL37A_CHICK.for.1946592-1947577.24.fasta -t /tmp/maker_6B3o0i/24/2284284.1946592-1947577.24.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/24/2284284.1946592-1947577.sp%7CP32046%7CRL37A_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
processing chunk output
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
collecting blastx repeatmasking
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing the chunk divide
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
doing repeat masking
choosing best annotation set
Choosing best annotations
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/0/2284529.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
choosing best annotation set
Choosing best annotations
collecting blastx reports
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CO73775%7CFBLN1_CHICK.for.951621-965756.9.fasta -t /tmp/maker_6B3o0i/9/2284529.951621-965756.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.951621-965756.sp%7CO73775%7CFBLN1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
choosing best annotation set
Choosing best annotations
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
processing all repeats
in cluster::shadow_cluster...
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1 -pa 1
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284727
Length: 1352482
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
prepare section files
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/1/2284289.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
collecting blastx reports
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
prepare section files
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
 ...processing 0 of 3
 ...processing 1 of 3
collecting blastx repeatmasking
 ...processing 2 of 3
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 4 of 5
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:-1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing all repeats
doing repeat masking
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
collecting blastx reports
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284529.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A7/9F/2284529//theVoid.2284529/1/2284529.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
doing repeat masking
Preparing evidence for hint based annotation
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
merging blast reports...
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
merging blast reports...
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP28127%7CWNT4_MELGA.for.1202635-1203803.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202635-1203803.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202635-1203803.sp%7CP28127%7CWNT4_MELGA.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP28128%7CWNT5A_MELGA.for.1202635-1203803.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202635-1203803.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202635-1203803.sp%7CP28128%7CWNT5A_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP28129%7CWNT7A_MELGA.for.1202635-1203803.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202635-1203803.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202635-1203803.sp%7CP28129%7CWNT7A_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ3L254%7CWNT7B_CHICK.for.1202572-1203851.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202572-1203851.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202572-1203851.sp%7CQ3L254%7CWNT7B_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP49339%7CWNT11_CHICK.for.1202572-1203881.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202572-1203881.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202572-1203881.sp%7CP49339%7CWNT11_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP28130%7CWNT7B_MELGA.for.1202635-1203803.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202635-1203803.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202635-1203803.sp%7CP28130%7CWNT7B_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ91029%7CWNT1_CHICK.for.1202599-1203887.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202599-1203887.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202599-1203887.sp%7CQ91029%7CWNT1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ98SN7%7CWNT2B_CHICK.for.1202572-1203833.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202572-1203833.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202572-1203833.sp%7CQ98SN7%7CWNT2B_CHICK.p.exonerate
#-------------------------------#
processing chunk output
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ2LMP1%7CWNT3A_CHICK.for.1202572-1203839.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202572-1203839.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202572-1203839.sp%7CQ2LMP1%7CWNT3A_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CO42280%7CWNT9A_CHICK.for.1202572-1203872.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202572-1203872.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202572-1203872.sp%7CO42280%7CWNT9A_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP28125%7CWNT3A_MELGA.for.1202635-1203803.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202635-1203803.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202635-1203803.sp%7CP28125%7CWNT3A_MELGA.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP28126%7CWNT3B_MELGA.for.1202635-1203803.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202635-1203803.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202635-1203803.sp%7CP28126%7CWNT3B_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP49337%7CWNT4_CHICK.for.1202572-1203836.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1202572-1203836.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1202572-1203836.sp%7CP49337%7CWNT4_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ3L254%7CWNT7B_CHICK.for.1231557-1232674.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1231557-1232674.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1231557-1232674.sp%7CQ3L254%7CWNT7B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ91029%7CWNT1_CHICK.for.1231554-1232674.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1231554-1232674.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1231554-1232674.sp%7CQ91029%7CWNT1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ98SN7%7CWNT2B_CHICK.for.1231581-1232674.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1231581-1232674.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1231581-1232674.sp%7CQ98SN7%7CWNT2B_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CQ2LMP1%7CWNT3A_CHICK.for.1231581-1232674.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1231581-1232674.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1231581-1232674.sp%7CQ2LMP1%7CWNT3A_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/9/sp%7CP49337%7CWNT4_CHICK.for.1231557-1232674.9.fasta -t /tmp/maker_6B3o0i/9/2284529.1231557-1232674.9.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/9/2284529.1231557-1232674.sp%7CP49337%7CWNT4_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
flattening protein clusters
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing the chunk divide
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
flattening protein clusters
doing blastx repeats
running  blast search.
merging blast reports...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
prepare section files
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
merging blast reports...
doing blastx repeats
running  blast search.
choosing best annotation set
Choosing best annotations
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
collecting blastx reports
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
processing chunk output
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Choosing best annotations
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
re-running blast for edge cases...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/37/blastprep/db.1481068-1512360.for_blastx.fasta
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.1481068-1512360.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.1481068.1512360.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.1481068.1512360.0.db%2E1481068-1512360%2Efor_blastx%2Efasta.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZJ00%7CEM55_CHICK.for.1490668-1502760.37.fasta -t /tmp/maker_6B3o0i/37/2284450.1490668-1502760.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.1490668-1502760.sp%7CQ5ZJ00%7CEM55_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/0/2284498.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
deleted:0 hits
merging blast reports...
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
processing chunk output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CP20785%7CCO6A1_CHICK.for.905582-907746.31.fasta -t /tmp/maker_6B3o0i/31/2284498.905582-907746.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.905582-907746.sp%7CP20785%7CCO6A1_CHICK.p.exonerate
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CP32017%7CCO9A3_CHICK.for.905606-907797.31.fasta -t /tmp/maker_6B3o0i/31/2284498.905606-907797.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.905606-907797.sp%7CP32017%7CCO9A3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284289.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5C/E5/2284289//theVoid.2284289/2/2284289.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
collecting blastx repeatmasking
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
merging blast reports...
merging blast reports...
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ7LZR2%7CCO8A1_CHICK.for.903319-908265.31.fasta -t /tmp/maker_6B3o0i/31/2284498.903319-908265.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.903319-908265.sp%7CQ7LZR2%7CCO8A1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing repeat masking
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
in cluster::shadow_cluster...
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:30   current j:0
 j_size:30   current j:1
 j_size:30   current j:2
 j_size:30   current j:3
 j_size:30   current j:4
 j_size:30   current j:5
 j_size:30   current j:6
 j_size:30   current j:7
 j_size:30   current j:8
 j_size:30   current j:9
 j_size:30   current j:10
 j_size:30   current j:11
 j_size:30   current j:12
 j_size:30   current j:13
 j_size:30   current j:14
 j_size:30   current j:15
 j_size:30   current j:16
 j_size:30   current j:17
 j_size:30   current j:18
 j_size:30   current j:19
 j_size:30   current j:20
 j_size:30   current j:21
 j_size:30   current j:22
 j_size:30   current j:23
 j_size:30   current j:24
 j_size:30   current j:25
 j_size:30   current j:26
 j_size:30   current j:27
 j_size:30   current j:28
 j_size:30   current j:29
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
polishing proteins
preparing masked sequence
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CP19596%7CFGF1_CHICK.for.418765-419753.20.fasta -t /tmp/maker_6B3o0i/20/2284543.418765-419753.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2284543.418765-419753.sp%7CP19596%7CFGF1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
examining contents of the fasta file and run log
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats



--Next Contig--

running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284742
Length: 7485617
#---------------------------------------------------------------------


doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
setting up GFF3 output and fasta chunks
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
prepare section files
deleted:0 hits
deleted:0 hits
preparing masked sequence
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
flattening protein clusters
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing the chunk divide
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
doing blastx repeats
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
prepare section files
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
gathering ab-init output files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
running  blast search.
processing all repeats
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP28673%7CNPY_CHICK.for.1662370-1669199.37.fasta -t /tmp/maker_6B3o0i/37/2284450.1662370-1669199.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.1662370-1669199.sp%7CP28673%7CNPY_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CP29203%7CPYY_CHICK.for.1668211-1669118.37.fasta -t /tmp/maker_6B3o0i/37/2284450.1668211-1669118.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.1668211-1669118.sp%7CP29203%7CPYY_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CP08125%7CCOAA1_CHICK.for.905693-907617.31.fasta -t /tmp/maker_6B3o0i/31/2284498.905693-907617.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.905693-907617.sp%7CP08125%7CCOAA1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
deleted:1 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
processing chunk output
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
choosing best annotation set
Choosing best annotations
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 10
 ...processing 1 of 10
 ...processing 2 of 10
 ...processing 3 of 10
 ...processing 4 of 10
 ...processing 5 of 10
 ...processing 6 of 10
 ...processing 7 of 10
 ...processing 8 of 10
 ...processing 9 of 10
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
merging blast reports...
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
processing chunk output
deleted:0 hits
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
prepare section files
collecting blastx reports
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
flattening protein clusters
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/3/2283926.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
choosing best annotation set
Choosing best annotations
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing all repeats
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1 -pa 1
#-------------------------------#
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
merging blast reports...
re-running blast for edge cases...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/32/blastprep/db.589453-628607.for_blastx.fasta
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.589453-628607.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.589453.628607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.589453.628607.0.db%2E589453-628607%2Efor_blastx%2Efasta.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/2/2284120.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
polishing proteins
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CO13016%7CPTN1_CHICK.for.599053-619007.32.fasta -t /tmp/maker_6B3o0i/32/2284461.599053-619007.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.599053-619007.sp%7CO13016%7CPTN1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
doing blastx repeats
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
flattening protein clusters
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
flattening protein clusters
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ5ZJV9%7CCNOT7_CHICK.for.616033-631889.20.fasta -t /tmp/maker_6B3o0i/20/2284543.616033-631889.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2284543.616033-631889.sp%7CQ5ZJV9%7CCNOT7_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ5F452%7CMTMR8_CHICK.for.670016-675788.20.fasta -t /tmp/maker_6B3o0i/20/2284543.670016-675788.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2284543.670016-675788.sp%7CQ5F452%7CMTMR8_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

flattening protein clusters
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284744
Length: 1773373
#---------------------------------------------------------------------


doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
prepare section files
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
examining contents of the fasta file and run log



--Next Contig--

deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284752
Length: 1576133
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
processing chunk output
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
doing blastx of proteins
running  blast search.
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CP79777%7CBRAC_CHICK.for.1139136-1150985.31.fasta -t /tmp/maker_6B3o0i/31/2284498.1139136-1150985.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.1139136-1150985.sp%7CP79777%7CBRAC_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CO73718%7CTBX3_CHICK.for.1145055-1148104.31.fasta -t /tmp/maker_6B3o0i/31/2284498.1145055-1148104.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.1145055-1148104.sp%7CO73718%7CTBX3_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CQ9PWE8%7CTBX5_CHICK.for.1145055-1148104.31.fasta -t /tmp/maker_6B3o0i/31/2284498.1145055-1148104.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.1145055-1148104.sp%7CQ9PWE8%7CTBX5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CP79779%7CTBX6L_CHICK.for.1145055-1146127.31.fasta -t /tmp/maker_6B3o0i/31/2284498.1145055-1146127.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.1145055-1146127.sp%7CP79779%7CTBX6L_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/31/sp%7CP79778%7CTBXT_CHICK.for.1139097-1152991.31.fasta -t /tmp/maker_6B3o0i/31/2284498.1139097-1152991.31.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/31/2284498.1139097-1152991.sp%7CP79778%7CTBXT_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
preparing masked sequence
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing ab-inits
prepare section files
flattening protein clusters
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
merging blast reports...
re-running blast for edge cases...
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/20/blastprep/db.678779-710188.for_blastx.fasta
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
gathering ab-init output files
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.678779-710188.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.678779.710188.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.678779.710188.0.db%2E678779-710188%2Efor_blastx%2Efasta.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
prepare section files
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
...finished
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
polishing proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ5F452%7CMTMR8_CHICK.for.688379-700588.20.fasta -t /tmp/maker_6B3o0i/20/2284543.688379-700588.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2284543.688379-700588.sp%7CQ5F452%7CMTMR8_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
cleaning blastx...
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/1/2284450.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing repeat masking
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/0/2284642.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
merging blast reports...
collecting blastx repeatmasking
deleted:0 hits
flattening protein clusters
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2 -pa 1
#-------------------------------#
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CB3TP03%7CCTR2_CHICK.for.807522-824799.20.fasta -t /tmp/maker_6B3o0i/20/2284543.807522-824799.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2284543.807522-824799.sp%7CB3TP03%7CCTR2_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
cleaning blastx...
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:3 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:3 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
re-running blast for edge cases...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/32/blastprep/db.884331-910929.for_blastx.fasta
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.884331-910929.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.884331.910929.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/0/2284461.884331.910929.0.db%2E884331-910929%2Efor_blastx%2Efasta.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
...finished
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CP09644%7CTBA5_CHICK.for.893997-895801.32.fasta -t /tmp/maker_6B3o0i/32/2284461.893997-895801.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.893997-895801.sp%7CP09644%7CTBA5_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CP09653%7CTBB5_CHICK.for.893931-901329.32.fasta -t /tmp/maker_6B3o0i/32/2284461.893931-901329.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.893931-901329.sp%7CP09653%7CTBB5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CP09652%7CTBB4_CHICK.for.893940-901329.32.fasta -t /tmp/maker_6B3o0i/32/2284461.893940-901329.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.893940-901329.sp%7CP09652%7CTBB4_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CP32882%7CTBB2_CHICK.for.893979-901329.32.fasta -t /tmp/maker_6B3o0i/32/2284461.893979-901329.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.893979-901329.sp%7CP32882%7CTBB2_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CP09203%7CTBB1_CHICK.for.893979-901329.32.fasta -t /tmp/maker_6B3o0i/32/2284461.893979-901329.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.893979-901329.sp%7CP09203%7CTBB1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CP09244%7CTBB7_CHICK.for.893982-901329.32.fasta -t /tmp/maker_6B3o0i/32/2284461.893982-901329.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.893982-901329.sp%7CP09244%7CTBB7_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CP09206%7CTBB3_CHICK.for.893982-901329.32.fasta -t /tmp/maker_6B3o0i/32/2284461.893982-901329.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.893982-901329.sp%7CP09206%7CTBB3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CP09207%7CTBB6_CHICK.for.893940-901329.32.fasta -t /tmp/maker_6B3o0i/32/2284461.893940-901329.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.893940-901329.sp%7CP09207%7CTBB6_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284498.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2C/09/2284498//theVoid.2284498/1/2284498.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/0/2284228.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP18461%7CFGFR2_CHICK.for.143377-146048.15.fasta -t /tmp/maker_6B3o0i/15/2284542.143377-146048.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.143377-146048.sp%7CP18461%7CFGFR2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ8AXY6%7CMUSK_CHICK.for.143009-146042.15.fasta -t /tmp/maker_6B3o0i/15/2284542.143009-146042.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.143009-146042.sp%7CQ8AXY6%7CMUSK_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
cleaning blastx...
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/0/2284543.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ804X6%7CFA9_CHICK.for.423636-437291.25.fasta -t /tmp/maker_6B3o0i/25/2284495.423636-437291.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.423636-437291.sp%7CQ804X6%7CFA9_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ90628%7CTRY2_CHICK.for.436228-437303.25.fasta -t /tmp/maker_6B3o0i/25/2284495.436228-437303.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.436228-437303.sp%7CQ90628%7CTRY2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ90629%7CTRY3_CHICK.for.436222-437303.25.fasta -t /tmp/maker_6B3o0i/25/2284495.436222-437303.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.436222-437303.sp%7CQ90629%7CTRY3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CP25155%7CFA10_CHICK.for.423645-437297.25.fasta -t /tmp/maker_6B3o0i/25/2284495.423645-437297.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.423645-437297.sp%7CP25155%7CFA10_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ90627%7CTRY1_CHICK.for.436228-437303.25.fasta -t /tmp/maker_6B3o0i/25/2284495.436228-437303.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.436228-437303.sp%7CQ90627%7CTRY1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing the chunk divide
collecting blastx reports
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:3 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
preparing evidence clusters for annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing repeat masking
deleted:0 hits
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284450.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/85/2284450//theVoid.2284450/2/2284450.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:2 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:2 hits
doing blastx of proteins
in cluster::shadow_cluster...
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CO42254%7CIF2B1_CHICK.for.2125348-2142928.37.fasta -t /tmp/maker_6B3o0i/37/2284450.2125348-2142928.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.2125348-2142928.sp%7CO42254%7CIF2B1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZLP8%7CIF2B3_CHICK.for.2125348-2140771.37.fasta -t /tmp/maker_6B3o0i/37/2284450.2125348-2140771.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.2125348-2140771.sp%7CQ5ZLP8%7CIF2B3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZLP8%7CIF2B3_CHICK.for.2166275-2176760.37.fasta -t /tmp/maker_6B3o0i/37/2284450.2166275-2176760.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.2166275-2176760.sp%7CQ5ZLP8%7CIF2B3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZI22%7CNUPL2_CHICK.for.2235511-2242833.37.fasta -t /tmp/maker_6B3o0i/37/2284450.2235511-2242833.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.2235511-2242833.sp%7CQ5ZI22%7CNUPL2_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/37/sp%7CQ5ZI33%7CKLHL7_CHICK.for.2254911-2275568.37.fasta -t /tmp/maker_6B3o0i/37/2284450.2254911-2275568.37.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/37/2284450.2254911-2275568.sp%7CQ5ZI33%7CKLHL7_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CQ5ZK82%7CMPPE1_CHICK.for.1010754-1031751.32.fasta -t /tmp/maker_6B3o0i/32/2284461.1010754-1031751.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.1010754-1031751.sp%7CQ5ZK82%7CMPPE1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
collecting blastx reports
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
merging blast reports...
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing the chunk divide
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
preparing evidence clusters for annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
collecting blastx reports
flattening protein clusters
merging blast reports...
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
total clusters:3 now processing 0
 ...processing 0 of 14
 ...processing 1 of 14
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
 ...processing 2 of 14
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 3 of 14
 ...processing 4 of 14
 ...processing 5 of 14
 ...processing 6 of 14
 ...processing 7 of 14
 ...processing 8 of 14
 ...processing 9 of 14
 ...processing 10 of 14
 ...processing 11 of 14
 ...processing 12 of 14
 ...processing 13 of 14
flattening protein clusters
 ...processing 0 of 16
 ...processing 1 of 16
 ...processing 2 of 16
 ...processing 3 of 16
 ...processing 4 of 16
 ...processing 5 of 16
 ...processing 6 of 16
 ...processing 7 of 16
 ...processing 8 of 16
 ...processing 9 of 16
 ...processing 10 of 16
 ...processing 11 of 16
 ...processing 12 of 16
 ...processing 13 of 16
 ...processing 14 of 16
 ...processing 15 of 16
total clusters:3 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
polishing proteins
merging blast reports...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ5ZLA6%7CMYO1C_CHICK.for.489620-497408.25.fasta -t /tmp/maker_6B3o0i/25/2284495.489620-497408.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.489620-497408.sp%7CQ5ZLA6%7CMYO1C_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ5ZMC2%7CMYO1G_CHICK.for.489632-497573.25.fasta -t /tmp/maker_6B3o0i/25/2284495.489632-497573.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.489632-497573.sp%7CQ5ZMC2%7CMYO1G_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 12
 ...processing 1 of 12
 ...processing 2 of 12
 ...processing 3 of 12
 ...processing 4 of 12
 ...processing 5 of 12
 ...processing 6 of 12
 ...processing 7 of 12
 ...processing 8 of 12
 ...processing 9 of 12
 ...processing 10 of 12
 ...processing 11 of 12
 ...processing 0 of 28
 ...processing 1 of 28
 ...processing 2 of 28
 ...processing 3 of 28
 ...processing 4 of 28
 ...processing 5 of 28
 ...processing 6 of 28
 ...processing 7 of 28
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 8 of 28
 ...processing 9 of 28
 ...processing 10 of 28
 ...processing 11 of 28
 ...processing 12 of 28
 ...processing 13 of 28
 ...processing 14 of 28
 ...processing 15 of 28
prepare section files
processing chunk output
 ...processing 16 of 28
 ...processing 17 of 28
 ...processing 18 of 28
 ...processing 19 of 28
 ...processing 20 of 28
 ...processing 21 of 28
 ...processing 22 of 28
 ...processing 23 of 28
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
 ...processing 24 of 28
 ...processing 25 of 28
 ...processing 26 of 28
 ...processing 27 of 28
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
deleted:0 hits
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
deleted:0 hits
prepare section files
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/2/2284220.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 14
 ...processing 1 of 14
 ...processing 2 of 14
 ...processing 3 of 14
 ...processing 4 of 14
 ...processing 5 of 14
 ...processing 6 of 14
 ...processing 7 of 14
 ...processing 8 of 14
doing blastx of proteins
 ...processing 9 of 14
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
 ...processing 10 of 14
 ...processing 11 of 14
 ...processing 12 of 14
 ...processing 13 of 14
 ...processing 0 of 10
 ...processing 1 of 10
 ...processing 2 of 10
 ...processing 3 of 10
 ...processing 4 of 10
 ...processing 5 of 10
choosing best annotation set
Choosing best annotations
 ...processing 6 of 10
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
 ...processing 7 of 10
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
 ...processing 8 of 10
deleted:0 hits
 ...processing 9 of 10
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing chunk output
annotating transcripts
Making transcripts
 ...processing 0 of 24
 ...processing 1 of 24
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 2 of 24
 ...processing 3 of 24
 ...processing 4 of 24
 ...processing 5 of 24
 ...processing 6 of 24
 ...processing 7 of 24
 ...processing 8 of 24
 ...processing 9 of 24
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
 ...processing 10 of 24
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 11 of 24
 ...processing 12 of 24
 ...processing 13 of 24
 ...processing 14 of 24
 ...processing 15 of 24
 ...processing 16 of 24
 ...processing 17 of 24
 ...processing 18 of 24
 ...processing 19 of 24
deleted:0 hits
deleted:0 hits
 ...processing 20 of 24
 ...processing 21 of 24
 ...processing 22 of 24
 ...processing 23 of 24
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Preparing evidence for hint based annotation
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
collecting blastx repeatmasking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
choosing best annotation set
Choosing best annotations
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
flattening protein clusters
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:-1 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3 -pa 1
#-------------------------------#
collecting blastx reports
deleted:0 hits
choosing best annotation set
Choosing best annotations
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
merging blast reports...
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing chunk output
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ02020%7CFIBB_CHICK.for.1081867-1090913.20.fasta -t /tmp/maker_6B3o0i/20/2284543.1081867-1090913.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2284543.1081867-1090913.sp%7CQ02020%7CFIBB_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ8AV28%7CPCM1_CHICK.for.1152532-1173362.20.fasta -t /tmp/maker_6B3o0i/20/2284543.1152532-1173362.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2284543.1152532-1173362.sp%7CQ8AV28%7CPCM1_CHICK.p.exonerate
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284753
Length: 5456262
#---------------------------------------------------------------------


deleted:0 hits
deleted:0 hits
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
cleaning blastx...
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:-1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/3/2283486.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ5ZK43%7CTM38A_CHICK.for.426542-429760.15.fasta -t /tmp/maker_6B3o0i/15/2284542.426542-429760.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.426542-429760.sp%7CQ5ZK43%7CTM38A_CHICK.p.exonerate
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
flattening protein clusters
collecting blastx reports
merging blast reports...
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx repeatmasking
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ5F3U0%7CSP130_CHICK.for.741367-750491.25.fasta -t /tmp/maker_6B3o0i/25/2284495.741367-750491.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.741367-750491.sp%7CQ5F3U0%7CSP130_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ5F3U0%7CSP130_CHICK.for.761365-770609.25.fasta -t /tmp/maker_6B3o0i/25/2284495.761365-770609.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.761365-770609.sp%7CQ5F3U0%7CSP130_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 10
 ...processing 1 of 10
 ...processing 2 of 10
 ...processing 3 of 10
doing repeat masking
 ...processing 4 of 10
 ...processing 5 of 10
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
 ...processing 6 of 10
 ...processing 7 of 10
 ...processing 8 of 10
 ...processing 9 of 10
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
polishing proteins
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/20/sp%7CQ8AV28%7CPCM1_CHICK.for.1183881-1196737.20.fasta -t /tmp/maker_6B3o0i/20/2284543.1183881-1196737.20.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/20/2284543.1183881-1196737.sp%7CQ8AV28%7CPCM1_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:2 hits
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:5 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
running  blast search.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
deleted:0 hits
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CO73691%7CEGR1_CHICK.for.580662-581638.15.fasta -t /tmp/maker_6B3o0i/15/2284542.580662-581638.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.580662-581638.sp%7CO73691%7CEGR1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
deleted:0 hits
deleted:0 hits
processing chunk output
collecting blastx reports
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CO73693%7CEGR1_TAEGU.for.580662-581638.15.fasta -t /tmp/maker_6B3o0i/15/2284542.580662-581638.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.580662-581638.sp%7CO73693%7CEGR1_TAEGU.p.exonerate
#-------------------------------#
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
polishing proteins
prepare section files
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CP02597%7CCALMS_CHICK.for.1292745-1293721.40.fasta -t /tmp/maker_6B3o0i/40/2284228.1292745-1293721.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.1292745-1293721.sp%7CP02597%7CCALMS_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CP05419%7CCALN_CHICK.for.1292745-1293703.40.fasta -t /tmp/maker_6B3o0i/40/2284228.1292745-1293703.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.1292745-1293703.sp%7CP05419%7CCALN_CHICK.p.exonerate
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CP62149%7CCALM_CHICK.for.1292745-1293703.40.fasta -t /tmp/maker_6B3o0i/40/2284228.1292745-1293703.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.1292745-1293703.sp%7CP62149%7CCALM_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284543.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/52/46/2284543//theVoid.2284543/1/2284543.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ76KB2%7CH6ST1_CHICK.for.886065-887572.25.fasta -t /tmp/maker_6B3o0i/25/2284495.886065-887572.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.886065-887572.sp%7CQ76KB2%7CH6ST1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ76LW2%7CH6ST2_CHICK.for.886065-887572.25.fasta -t /tmp/maker_6B3o0i/25/2284495.886065-887572.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.886065-887572.sp%7CQ76LW2%7CH6ST2_CHICK.p.exonerate
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing the chunk divide
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
doing blastx repeats
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/0/2284554.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing contig output
collecting blastx reports
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking



--Next Contig--

polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ5ZMP6%7CAP2M1_CHICK.for.617456-619736.15.fasta -t /tmp/maker_6B3o0i/15/2284542.617456-619736.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.617456-619736.sp%7CQ5ZMP6%7CAP2M1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284760
Length: 4217561
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ5ZMP7%7CAP3M1_CHICK.for.617426-619772.15.fasta -t /tmp/maker_6B3o0i/15/2284542.617426-619772.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.617426-619772.sp%7CQ5ZMP7%7CAP3M1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
setting up GFF3 output and fasta chunks
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ5F470%7CRAB8A_CHICK.for.641664-645392.15.fasta -t /tmp/maker_6B3o0i/15/2284542.641664-645392.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.641664-645392.sp%7CQ5F470%7CRAB8A_CHICK.p.exonerate
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP04268%7CTPM1_CHICK.for.653438-667277.15.fasta -t /tmp/maker_6B3o0i/15/2284542.653438-667277.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.653438-667277.sp%7CP04268%7CTPM1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP19352%7CTPM2_CHICK.for.653438-667277.15.fasta -t /tmp/maker_6B3o0i/15/2284542.653438-667277.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.653438-667277.sp%7CP19352%7CTPM2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:2 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/0/2284495.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
doing blastx of proteins
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:29   current j:0
 j_size:29   current j:1
 j_size:29   current j:2
 j_size:29   current j:3
 j_size:29   current j:4
 j_size:29   current j:5
 j_size:29   current j:6
 j_size:29   current j:7
 j_size:29   current j:8
 j_size:29   current j:9
 j_size:29   current j:10
 j_size:29   current j:11
 j_size:29   current j:12
 j_size:29   current j:13
 j_size:29   current j:14
 j_size:29   current j:15
 j_size:29   current j:16
 j_size:29   current j:17
 j_size:29   current j:18
 j_size:29   current j:19
 j_size:29   current j:20
 j_size:29   current j:21
 j_size:29   current j:22
 j_size:29   current j:23
 j_size:29   current j:24
 j_size:29   current j:25
 j_size:29   current j:26
 j_size:29   current j:27
 j_size:29   current j:28
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
doing blastx of proteins
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
choosing best annotation set
Choosing best annotations
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
doing blastx repeats
running  repeat masker.
running  blast search.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:32   current j:0
 j_size:32   current j:1
 j_size:32   current j:2
 j_size:32   current j:3
 j_size:32   current j:4
 j_size:32   current j:5
 j_size:32   current j:6
 j_size:32   current j:7
 j_size:32   current j:8
 j_size:32   current j:9
 j_size:32   current j:10
 j_size:32   current j:11
 j_size:32   current j:12
 j_size:32   current j:13
 j_size:32   current j:14
 j_size:32   current j:15
 j_size:32   current j:16
 j_size:32   current j:17
 j_size:32   current j:18
 j_size:32   current j:19
 j_size:32   current j:20
 j_size:32   current j:21
 j_size:32   current j:22
 j_size:32   current j:23
 j_size:32   current j:24
 j_size:32   current j:25
 j_size:32   current j:26
 j_size:32   current j:27
 j_size:32   current j:28
 j_size:32   current j:29
 j_size:32   current j:30
 j_size:32   current j:31
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
preparing masked sequence
annotating transcripts
Making transcripts
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
preparing ab-inits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1 -pa 1
#-------------------------------#
deleted:0 hits
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
gathering ab-init output files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ5ZIY4%7CSBDS_CHICK.for.1576081-1579406.40.fasta -t /tmp/maker_6B3o0i/40/2284228.1576081-1579406.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.1576081-1579406.sp%7CQ5ZIY4%7CSBDS_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
cleaning blastx...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/1/2284509.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
doing repeat masking
Processing transcripts into genes
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284554.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/CB/05/2284554//theVoid.2284554/1/2284554.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx repeatmasking
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
re-running blast for edge cases...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/40/blastprep/db.1589016-1612197.for_blastx.fasta
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing the chunk divide
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.1589016-1612197.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.1589016.1612197.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.1589016.1612197.0.db%2E1589016-1612197%2Efor_blastx%2Efasta.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ5ZMH1%7CSEPT2_CHICK.for.1598616-1602597.40.fasta -t /tmp/maker_6B3o0i/40/2284228.1598616-1602597.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.1598616-1602597.sp%7CQ5ZMH1%7CSEPT2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CP53666%7CLIMK2_CHICK.for.1617989-1623213.40.fasta -t /tmp/maker_6B3o0i/40/2284228.1617989-1623213.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.1617989-1623213.sp%7CP53666%7CLIMK2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ8QFP8%7CLIMK1_CHICK.for.1617980-1623207.40.fasta -t /tmp/maker_6B3o0i/40/2284228.1617980-1623207.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.1617980-1623207.sp%7CQ8QFP8%7CLIMK1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ76KB2%7CH6ST1_CHICK.for.1136213-1137531.25.fasta -t /tmp/maker_6B3o0i/25/2284495.1136213-1137531.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.1136213-1137531.sp%7CQ76KB2%7CH6ST1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/25/sp%7CQ76LW2%7CH6ST2_CHICK.for.1136201-1137510.25.fasta -t /tmp/maker_6B3o0i/25/2284495.1136201-1137510.25.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/25/2284495.1136201-1137510.sp%7CQ76LW2%7CH6ST2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
doing blastx of proteins
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing chunk output
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
deleted:0 hits
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/0/2284542.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
merging blast reports...
merging blast reports...
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:30   current j:0
 j_size:30   current j:1
 j_size:30   current j:2
 j_size:30   current j:3
 j_size:30   current j:4
 j_size:30   current j:5
 j_size:30   current j:6
 j_size:30   current j:7
 j_size:30   current j:8
 j_size:30   current j:9
 j_size:30   current j:10
 j_size:30   current j:11
 j_size:30   current j:12
 j_size:30   current j:13
 j_size:30   current j:14
 j_size:30   current j:15
 j_size:30   current j:16
 j_size:30   current j:17
 j_size:30   current j:18
 j_size:30   current j:19
 j_size:30   current j:20
 j_size:30   current j:21
 j_size:30   current j:22
 j_size:30   current j:23
 j_size:30   current j:24
 j_size:30   current j:25
 j_size:30   current j:26
 j_size:30   current j:27
 j_size:30   current j:28
 j_size:30   current j:29
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
clustering transcripts into genes for annotations
Processing transcripts into genes
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
processing chunk output
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284765
Length: 2356700
#---------------------------------------------------------------------


deleted:0 hits
setting up GFF3 output and fasta chunks
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx reports
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
merging blast reports...
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
processing contig output
running  blast search.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284776
Length: 2993008
#---------------------------------------------------------------------


doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
setting up GFF3 output and fasta chunks
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/1/2284461.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0 -pa 1
#-------------------------------#
flattening protein clusters
processing all repeats
doing blastx of proteins
running  blast search.
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:37   current j:0
 j_size:37   current j:1
 j_size:37   current j:2
 j_size:37   current j:3
 j_size:37   current j:4
 j_size:37   current j:5
 j_size:37   current j:6
 j_size:37   current j:7
 j_size:37   current j:8
 j_size:37   current j:9
 j_size:37   current j:10
 j_size:37   current j:11
 j_size:37   current j:12
 j_size:37   current j:13
 j_size:37   current j:14
 j_size:37   current j:15
 j_size:37   current j:16
 j_size:37   current j:17
 j_size:37   current j:18
 j_size:37   current j:19
 j_size:37   current j:20
 j_size:37   current j:21
 j_size:37   current j:22
 j_size:37   current j:23
 j_size:37   current j:24
 j_size:37   current j:25
 j_size:37   current j:26
 j_size:37   current j:27
 j_size:37   current j:28
 j_size:37   current j:29
 j_size:37   current j:30
 j_size:37   current j:31
 j_size:37   current j:32
 j_size:37   current j:33
 j_size:37   current j:34
 j_size:37   current j:35
 j_size:37   current j:36
...finished clustering.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ90687%7CPTN11_CHICK.for.1146531-1157698.15.fasta -t /tmp/maker_6B3o0i/15/2284542.1146531-1157698.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.1146531-1157698.sp%7CQ90687%7CPTN11_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CO13016%7CPTN1_CHICK.for.1146531-1148478.15.fasta -t /tmp/maker_6B3o0i/15/2284542.1146531-1148478.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.1146531-1148478.sp%7CO13016%7CPTN1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1 -pa 1
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ5F383%7CSPP2B_CHICK.for.330455-332134.29.fasta -t /tmp/maker_6B3o0i/29/2284622.330455-332134.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.330455-332134.sp%7CQ5F383%7CSPP2B_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/1/2284228.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing ab-inits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
collecting blastx reports
doing blastx of proteins
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
prepare section files
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
collecting blastx reports
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
collecting blastx reports
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing contig output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
collecting blastx repeatmasking
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP08023%7CACTA_CHICK.for.29286-33058.18.fasta -t /tmp/maker_6B3o0i/18/2284366.29286-33058.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.29286-33058.sp%7CP08023%7CACTA_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP60706%7CACTB_CHICK.for.29286-33058.18.fasta -t /tmp/maker_6B3o0i/18/2284366.29286-33058.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.29286-33058.sp%7CP60706%7CACTB_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP68034%7CACTC_CHICK.for.29286-33058.18.fasta -t /tmp/maker_6B3o0i/18/2284366.29286-33058.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.29286-33058.sp%7CP68034%7CACTC_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZMQ2%7CACTG_CHICK.for.29286-33058.18.fasta -t /tmp/maker_6B3o0i/18/2284366.29286-33058.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.29286-33058.sp%7CQ5ZMQ2%7CACTG_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP53488%7CARP2_CHICK.for.29295-33049.18.fasta -t /tmp/maker_6B3o0i/18/2284366.29295-33049.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.29295-33049.sp%7CP53488%7CARP2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP63270%7CACTH_CHICK.for.29286-33058.18.fasta -t /tmp/maker_6B3o0i/18/2284366.29286-33058.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.29286-33058.sp%7CP63270%7CACTH_CHICK.p.exonerate
#-------------------------------#
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP68139%7CACTS_CHICK.for.29286-33058.18.fasta -t /tmp/maker_6B3o0i/18/2284366.29286-33058.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.29286-33058.sp%7CP68139%7CACTS_CHICK.p.exonerate
#-------------------------------#
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP53478%7CACT5_CHICK.for.29286-33058.18.fasta -t /tmp/maker_6B3o0i/18/2284366.29286-33058.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.29286-33058.sp%7CP53478%7CACT5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
cleaning blastx...
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats



--Next Contig--

in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284777
Length: 2451710
#---------------------------------------------------------------------


Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
prepare section files
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2 -pa 1
#-------------------------------#
merging blast reports...
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ8QFX1%7CRIMB2_CHICK.for.2049259-2057920.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2049259-2057920.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2049259-2057920.sp%7CQ8QFX1%7CRIMB2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/0/2284673.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/3/2284347.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
collecting blastx reports
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
flattening protein clusters
doing repeat masking
collecting blastx reports
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:43   current j:0
 j_size:43   current j:1
 j_size:43   current j:2
 j_size:43   current j:3
 j_size:43   current j:4
 j_size:43   current j:5
 j_size:43   current j:6
 j_size:43   current j:7
 j_size:43   current j:8
 j_size:43   current j:9
 j_size:43   current j:10
 j_size:43   current j:11
 j_size:43   current j:12
 j_size:43   current j:13
 j_size:43   current j:14
 j_size:43   current j:15
 j_size:43   current j:16
 j_size:43   current j:17
 j_size:43   current j:18
 j_size:43   current j:19
 j_size:43   current j:20
 j_size:43   current j:21
 j_size:43   current j:22
 j_size:43   current j:23
 j_size:43   current j:24
 j_size:43   current j:25
 j_size:43   current j:26
 j_size:43   current j:27
 j_size:43   current j:28
 j_size:43   current j:29
 j_size:43   current j:30
 j_size:43   current j:31
 j_size:43   current j:32
 j_size:43   current j:33
 j_size:43   current j:34
 j_size:43   current j:35
 j_size:43   current j:36
 j_size:43   current j:37
 j_size:43   current j:38
 j_size:43   current j:39
 j_size:43   current j:40
 j_size:43   current j:41
 j_size:43   current j:42
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:3 hits
collecting blastx reports
deleted:0 hits
merging blast reports...
deleted:0 hits
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:3 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
deleted:0 hits
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:-3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:-3 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-3 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284542.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/44/2284542//theVoid.2284542/1/2284542.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:-2 hits
collecting blastx reports
processing all repeats
collecting blastx repeatmasking
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ91955%7CMTPN_CHICK.for.1416976-1418231.15.fasta -t /tmp/maker_6B3o0i/15/2284542.1416976-1418231.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.1416976-1418231.sp%7CQ91955%7CMTPN_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ90686%7CCATK_CHICK.for.1504554-1505854.15.fasta -t /tmp/maker_6B3o0i/15/2284542.1504554-1505854.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.1504554-1505854.sp%7CQ90686%7CCATK_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CP09648%7CCATL1_CHICK.for.1504554-1505920.15.fasta -t /tmp/maker_6B3o0i/15/2284542.1504554-1505920.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.1504554-1505920.sp%7CP09648%7CCATL1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ5ZJU8%7CTP8L1_CHICK.for.1520633-1521990.15.fasta -t /tmp/maker_6B3o0i/15/2284542.1520633-1521990.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.1520633-1521990.sp%7CQ5ZJU8%7CTP8L1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/15/sp%7CQ5ZI78%7CTFIP8_CHICK.for.1520633-1521987.15.fasta -t /tmp/maker_6B3o0i/15/2284542.1520633-1521987.15.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/15/2284542.1520633-1521987.sp%7CQ5ZI78%7CTFIP8_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
merging blast reports...
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CB5FX56%7CCCD58_TAEGU.for.625422-627029.29.fasta -t /tmp/maker_6B3o0i/29/2284622.625422-627029.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.625422-627029.sp%7CB5FX56%7CCCD58_TAEGU.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ5ZML1%7CIMA5_CHICK.for.658928-662420.29.fasta -t /tmp/maker_6B3o0i/29/2284622.658928-662420.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.658928-662420.sp%7CQ5ZML1%7CIMA5_CHICK.p.exonerate
#-------------------------------#
deleted:-3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:-1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0 -pa 1
#-------------------------------#
processing the chunk divide
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37067%7COLF1_CHICK.for.11108-12819.7.fasta -t /tmp/maker_6B3o0i/7/2284347.11108-12819.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.11108-12819.sp%7CP37067%7COLF1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37068%7COLF2_CHICK.for.11108-12819.7.fasta -t /tmp/maker_6B3o0i/7/2284347.11108-12819.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.11108-12819.sp%7CP37068%7COLF2_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37069%7COLF3_CHICK.for.11108-12819.7.fasta -t /tmp/maker_6B3o0i/7/2284347.11108-12819.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.11108-12819.sp%7CP37069%7COLF3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37070%7COLF4_CHICK.for.11108-12819.7.fasta -t /tmp/maker_6B3o0i/7/2284347.11108-12819.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.11108-12819.sp%7CP37070%7COLF4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37071%7COLF5_CHICK.for.11108-12819.7.fasta -t /tmp/maker_6B3o0i/7/2284347.11108-12819.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.11108-12819.sp%7CP37071%7COLF5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37067%7COLF1_CHICK.for.15427-16607.7.fasta -t /tmp/maker_6B3o0i/7/2284347.15427-16607.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.15427-16607.sp%7CP37067%7COLF1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37068%7COLF2_CHICK.for.15427-16607.7.fasta -t /tmp/maker_6B3o0i/7/2284347.15427-16607.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.15427-16607.sp%7CP37068%7COLF2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37069%7COLF3_CHICK.for.15427-16607.7.fasta -t /tmp/maker_6B3o0i/7/2284347.15427-16607.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.15427-16607.sp%7CP37069%7COLF3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37070%7COLF4_CHICK.for.15427-16607.7.fasta -t /tmp/maker_6B3o0i/7/2284347.15427-16607.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.15427-16607.sp%7CP37070%7COLF4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37071%7COLF5_CHICK.for.15427-16604.7.fasta -t /tmp/maker_6B3o0i/7/2284347.15427-16604.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.15427-16604.sp%7CP37071%7COLF5_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37072%7COLF6_CHICK.for.15427-16607.7.fasta -t /tmp/maker_6B3o0i/7/2284347.15427-16607.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.15427-16607.sp%7CP37072%7COLF6_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98913%7COLF8_CHICK.for.64374-75244.7.fasta -t /tmp/maker_6B3o0i/7/2284347.64374-75244.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.64374-75244.sp%7CQ98913%7COLF8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98914%7COLF9_CHICK.for.64455-75244.7.fasta -t /tmp/maker_6B3o0i/7/2284347.64455-75244.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.64455-75244.sp%7CQ98914%7COLF9_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37067%7COLF1_CHICK.for.64308-75512.7.fasta -t /tmp/maker_6B3o0i/7/2284347.64308-75512.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.64308-75512.sp%7CP37067%7COLF1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37068%7COLF2_CHICK.for.64290-75494.7.fasta -t /tmp/maker_6B3o0i/7/2284347.64290-75494.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.64290-75494.sp%7CP37068%7COLF2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37069%7COLF3_CHICK.for.64308-75494.7.fasta -t /tmp/maker_6B3o0i/7/2284347.64308-75494.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.64308-75494.sp%7CP37069%7COLF3_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37070%7COLF4_CHICK.for.64290-75512.7.fasta -t /tmp/maker_6B3o0i/7/2284347.64290-75512.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.64290-75512.sp%7CP37070%7COLF4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37071%7COLF5_CHICK.for.64290-75512.7.fasta -t /tmp/maker_6B3o0i/7/2284347.64290-75512.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.64290-75512.sp%7CP37071%7COLF5_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37072%7COLF6_CHICK.for.64302-75449.7.fasta -t /tmp/maker_6B3o0i/7/2284347.64302-75449.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.64302-75449.sp%7CP37072%7COLF6_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
total clusters:2 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
total clusters:3 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284495.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D1/A9/2284495//theVoid.2284495/1/2284495.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ90826%7CCCL4_CHICK.for.2203942-2205285.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2203942-2205285.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2203942-2205285.sp%7CQ90826%7CCCL4_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:-2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:-2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
processing the chunk divide
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CQ5R2I8%7CAPCD1_CHICK.for.2380795-2383716.32.fasta -t /tmp/maker_6B3o0i/32/2284461.2380795-2383716.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.2380795-2383716.sp%7CQ5R2I8%7CAPCD1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
cleaning blastx...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:-1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
merging blast reports...
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:-1 hits
doing blastx repeats
deleted:1 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP19439%7CGLRK_CHICK.for.362621-374998.18.fasta -t /tmp/maker_6B3o0i/18/2284366.362621-374998.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.362621-374998.sp%7CP19439%7CGLRK_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
flattening protein clusters
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ5ZML1%7CIMA5_CHICK.for.673036-694421.29.fasta -t /tmp/maker_6B3o0i/29/2284622.673036-694421.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.673036-694421.sp%7CQ5ZML1%7CIMA5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ92075%7CSCNNA_CHICK.for.771230-778706.29.fasta -t /tmp/maker_6B3o0i/29/2284622.771230-778706.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.771230-778706.sp%7CQ92075%7CSCNNA_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:-1 hits
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx reports
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/0/2284688.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37069%7COLF3_CHICK.for.90812-92127.7.fasta -t /tmp/maker_6B3o0i/7/2284347.90812-92127.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.90812-92127.sp%7CP37069%7COLF3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37068%7COLF2_CHICK.for.90812-92127.7.fasta -t /tmp/maker_6B3o0i/7/2284347.90812-92127.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.90812-92127.sp%7CP37068%7COLF2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37072%7COLF6_CHICK.for.90812-92127.7.fasta -t /tmp/maker_6B3o0i/7/2284347.90812-92127.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.90812-92127.sp%7CP37072%7COLF6_CHICK.p.exonerate
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37071%7COLF5_CHICK.for.90812-92127.7.fasta -t /tmp/maker_6B3o0i/7/2284347.90812-92127.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.90812-92127.sp%7CP37071%7COLF5_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37070%7COLF4_CHICK.for.90812-92520.7.fasta -t /tmp/maker_6B3o0i/7/2284347.90812-92520.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.90812-92520.sp%7CP37070%7COLF4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37069%7COLF3_CHICK.for.108459-110170.7.fasta -t /tmp/maker_6B3o0i/7/2284347.108459-110170.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.108459-110170.sp%7CP37069%7COLF3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37068%7COLF2_CHICK.for.108459-110170.7.fasta -t /tmp/maker_6B3o0i/7/2284347.108459-110170.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.108459-110170.sp%7CP37068%7COLF2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98914%7COLF9_CHICK.for.108609-109801.7.fasta -t /tmp/maker_6B3o0i/7/2284347.108609-109801.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.108609-109801.sp%7CQ98914%7COLF9_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37072%7COLF6_CHICK.for.108462-110170.7.fasta -t /tmp/maker_6B3o0i/7/2284347.108462-110170.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.108462-110170.sp%7CP37072%7COLF6_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37067%7COLF1_CHICK.for.108459-110170.7.fasta -t /tmp/maker_6B3o0i/7/2284347.108459-110170.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.108459-110170.sp%7CP37067%7COLF1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37071%7COLF5_CHICK.for.108453-110170.7.fasta -t /tmp/maker_6B3o0i/7/2284347.108453-110170.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.108453-110170.sp%7CP37071%7COLF5_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37070%7COLF4_CHICK.for.108453-110170.7.fasta -t /tmp/maker_6B3o0i/7/2284347.108453-110170.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.108453-110170.sp%7CP37070%7COLF4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98913%7COLF8_CHICK.for.162883-164153.7.fasta -t /tmp/maker_6B3o0i/7/2284347.162883-164153.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.162883-164153.sp%7CQ98913%7COLF8_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98914%7COLF9_CHICK.for.162964-164153.7.fasta -t /tmp/maker_6B3o0i/7/2284347.162964-164153.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.162964-164153.sp%7CQ98914%7COLF9_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37067%7COLF1_CHICK.for.162817-164510.7.fasta -t /tmp/maker_6B3o0i/7/2284347.162817-164510.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.162817-164510.sp%7CP37067%7COLF1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37068%7COLF2_CHICK.for.162817-164510.7.fasta -t /tmp/maker_6B3o0i/7/2284347.162817-164510.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.162817-164510.sp%7CP37068%7COLF2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37069%7COLF3_CHICK.for.162817-164510.7.fasta -t /tmp/maker_6B3o0i/7/2284347.162817-164510.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.162817-164510.sp%7CP37069%7COLF3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37070%7COLF4_CHICK.for.162817-164510.7.fasta -t /tmp/maker_6B3o0i/7/2284347.162817-164510.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.162817-164510.sp%7CP37070%7COLF4_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37071%7COLF5_CHICK.for.162817-164510.7.fasta -t /tmp/maker_6B3o0i/7/2284347.162817-164510.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.162817-164510.sp%7CP37071%7COLF5_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37072%7COLF6_CHICK.for.162817-164510.7.fasta -t /tmp/maker_6B3o0i/7/2284347.162817-164510.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.162817-164510.sp%7CP37072%7COLF6_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98913%7COLF8_CHICK.for.179165-180441.7.fasta -t /tmp/maker_6B3o0i/7/2284347.179165-180441.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.179165-180441.sp%7CQ98913%7COLF8_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98914%7COLF9_CHICK.for.179246-180441.7.fasta -t /tmp/maker_6B3o0i/7/2284347.179246-180441.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.179246-180441.sp%7CQ98914%7COLF9_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
total clusters:4 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
total clusters:4 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
total clusters:4 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
total clusters:4 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ9PWH2%7CFZD10_CHICK.for.2362338-2364751.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2362338-2364751.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2362338-2364751.sp%7CQ9PWH2%7CFZD10_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CO57328%7CFZD1_CHICK.for.2362338-2364616.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2362338-2364616.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2362338-2364616.sp%7CO57328%7CFZD1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing masked sequence
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ9IA06%7CFZD2_CHICK.for.2362338-2364631.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2362338-2364631.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2362338-2364631.sp%7CQ9IA06%7CFZD2_CHICK.p.exonerate
#-------------------------------#
collecting blastx repeatmasking
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ9IA96%7CSFRP2_CHICK.for.2362338-2363440.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2362338-2363440.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2362338-2363440.sp%7CQ9IA96%7CSFRP2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ9PTW3%7CFZD3_CHICK.for.2362977-2363995.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2362977-2363995.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2362977-2363995.sp%7CQ9PTW3%7CFZD3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ9IA05%7CFZD4_CHICK.for.2362338-2364616.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2362338-2364616.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2362338-2364616.sp%7CQ9IA05%7CFZD4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CO57329%7CFZD7_CHICK.for.2362338-2364643.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2362338-2364643.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2362338-2364643.sp%7CO57329%7CFZD7_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ9IA03%7CFZD8_CHICK.for.2363118-2364535.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2363118-2364535.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2363118-2364535.sp%7CQ9IA03%7CFZD8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CQ9IA02%7CFZD9_CHICK.for.2362776-2364751.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2362776-2364751.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2362776-2364751.sp%7CQ9IA02%7CFZD9_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
preparing ab-inits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing repeat masking
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:4 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
re-running blast for edge cases...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/32/blastprep/db.2387686-2410563.for_blastx.fasta
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.2387686-2410563.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.2387686.2410563.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.2387686.2410563.0.db%2E2387686-2410563%2Efor_blastx%2Efasta.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
...finished
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/32/sp%7CQ5R2I8%7CAPCD1_CHICK.for.2397286-2400963.32.fasta -t /tmp/maker_6B3o0i/32/2284461.2397286-2400963.32.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/32/2284461.2397286-2400963.sp%7CQ5R2I8%7CAPCD1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
preparing ab-inits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ2VRL0%7CPLCZ1_CHICK.for.406963-418800.18.fasta -t /tmp/maker_6B3o0i/18/2284366.406963-418800.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.406963-418800.sp%7CQ2VRL0%7CPLCZ1_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
deleted:0 hits
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
prepare section files
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/3/2284436.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ5ZKG1%7CRM51_CHICK.for.791317-792739.29.fasta -t /tmp/maker_6B3o0i/29/2284622.791317-792739.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.791317-792739.sp%7CQ5ZKG1%7CRM51_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP00356%7CG3P_CHICK.for.847025-850066.29.fasta -t /tmp/maker_6B3o0i/29/2284622.847025-850066.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.847025-850066.sp%7CP00356%7CG3P_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CO57479%7CG3P_COLLI.for.847025-850492.29.fasta -t /tmp/maker_6B3o0i/29/2284622.847025-850492.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.847025-850492.sp%7CO57479%7CG3P_COLLI.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CO57672%7CG3P_MELGA.for.847849-850066.29.fasta -t /tmp/maker_6B3o0i/29/2284622.847849-850066.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.847849-850066.sp%7CO57672%7CG3P_MELGA.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:2 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284228.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5E/8C/2284228//theVoid.2284228/2/2284228.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
prepare section files
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37069%7COLF3_CHICK.for.201085-202787.7.fasta -t /tmp/maker_6B3o0i/7/2284347.201085-202787.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.201085-202787.sp%7CP37069%7COLF3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37068%7COLF2_CHICK.for.201085-202787.7.fasta -t /tmp/maker_6B3o0i/7/2284347.201085-202787.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.201085-202787.sp%7CP37068%7COLF2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98914%7COLF9_CHICK.for.201445-202631.7.fasta -t /tmp/maker_6B3o0i/7/2284347.201445-202631.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.201445-202631.sp%7CQ98914%7COLF9_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37072%7COLF6_CHICK.for.201085-202784.7.fasta -t /tmp/maker_6B3o0i/7/2284347.201085-202784.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.201085-202784.sp%7CP37072%7COLF6_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:3 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37067%7COLF1_CHICK.for.201085-202787.7.fasta -t /tmp/maker_6B3o0i/7/2284347.201085-202787.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.201085-202787.sp%7CP37067%7COLF1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37071%7COLF5_CHICK.for.201079-202790.7.fasta -t /tmp/maker_6B3o0i/7/2284347.201079-202790.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.201079-202790.sp%7CP37071%7COLF5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37070%7COLF4_CHICK.for.201085-202790.7.fasta -t /tmp/maker_6B3o0i/7/2284347.201085-202790.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.201085-202790.sp%7CP37070%7COLF4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98913%7COLF8_CHICK.for.201445-202718.7.fasta -t /tmp/maker_6B3o0i/7/2284347.201445-202718.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.201445-202718.sp%7CQ98913%7COLF8_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98913%7COLF8_CHICK.for.210155-211431.7.fasta -t /tmp/maker_6B3o0i/7/2284347.210155-211431.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.210155-211431.sp%7CQ98913%7COLF8_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ98914%7COLF9_CHICK.for.210239-211431.7.fasta -t /tmp/maker_6B3o0i/7/2284347.210239-211431.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.210239-211431.sp%7CQ98914%7COLF9_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37067%7COLF1_CHICK.for.210083-211800.7.fasta -t /tmp/maker_6B3o0i/7/2284347.210083-211800.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.210083-211800.sp%7CP37067%7COLF1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37068%7COLF2_CHICK.for.210083-211800.7.fasta -t /tmp/maker_6B3o0i/7/2284347.210083-211800.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.210083-211800.sp%7CP37068%7COLF2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37069%7COLF3_CHICK.for.210083-211800.7.fasta -t /tmp/maker_6B3o0i/7/2284347.210083-211800.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.210083-211800.sp%7CP37069%7COLF3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37070%7COLF4_CHICK.for.210083-211800.7.fasta -t /tmp/maker_6B3o0i/7/2284347.210083-211800.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.210083-211800.sp%7CP37070%7COLF4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37071%7COLF5_CHICK.for.210083-211800.7.fasta -t /tmp/maker_6B3o0i/7/2284347.210083-211800.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.210083-211800.sp%7CP37071%7COLF5_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP37072%7COLF6_CHICK.for.210083-211800.7.fasta -t /tmp/maker_6B3o0i/7/2284347.210083-211800.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.210083-211800.sp%7CP37072%7COLF6_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
total clusters:2 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
total clusters:2 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
doing blastx repeats
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
running  blast search.
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
choosing best annotation set
Choosing best annotations
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
doing repeat masking
polishing proteins
preparing evidence clusters for annotations
in cluster::shadow_cluster...
Preparing evidence for hint based annotation
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/40/sp%7CE1C3U7%7CLOXL2_CHICK.for.2457747-2458919.40.fasta -t /tmp/maker_6B3o0i/40/2284228.2457747-2458919.40.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/40/2284228.2457747-2458919.sp%7CE1C3U7%7CLOXL2_CHICK.p.exonerate
#-------------------------------#
processing chunk output
prepare section files
cleaning blastx...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
flattening protein clusters
deleted:5 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing the chunk divide
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
choosing best annotation set
Choosing best annotations
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZHM5%7CRER1_CHICK.for.541650-545402.18.fasta -t /tmp/maker_6B3o0i/18/2284366.541650-545402.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.541650-545402.sp%7CQ5ZHM5%7CRER1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/0/2284622.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
preparing evidence clusters for annotations
doing blastx repeats
Preparing evidence for hint based annotation
running  blast search.
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing all repeats
collecting blastx reports
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CB6ZLK2%7CCHD1_CHICK.for.900515-907502.29.fasta -t /tmp/maker_6B3o0i/29/2284622.900515-907502.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.900515-907502.sp%7CB6ZLK2%7CCHD1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP28127%7CWNT4_MELGA.for.961353-962509.29.fasta -t /tmp/maker_6B3o0i/29/2284622.961353-962509.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.961353-962509.sp%7CP28127%7CWNT4_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP28128%7CWNT5A_MELGA.for.961353-962509.29.fasta -t /tmp/maker_6B3o0i/29/2284622.961353-962509.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.961353-962509.sp%7CP28128%7CWNT5A_MELGA.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP28129%7CWNT7A_MELGA.for.961353-962509.29.fasta -t /tmp/maker_6B3o0i/29/2284622.961353-962509.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.961353-962509.sp%7CP28129%7CWNT7A_MELGA.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP49339%7CWNT11_CHICK.for.960460-962572.29.fasta -t /tmp/maker_6B3o0i/29/2284622.960460-962572.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.960460-962572.sp%7CP49339%7CWNT11_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ3L254%7CWNT7B_CHICK.for.959547-962572.29.fasta -t /tmp/maker_6B3o0i/29/2284622.959547-962572.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.959547-962572.sp%7CQ3L254%7CWNT7B_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ91029%7CWNT1_CHICK.for.959553-962542.29.fasta -t /tmp/maker_6B3o0i/29/2284622.959553-962542.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.959553-962542.sp%7CQ91029%7CWNT1_CHICK.p.exonerate
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP28130%7CWNT7B_MELGA.for.961353-962509.29.fasta -t /tmp/maker_6B3o0i/29/2284622.961353-962509.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.961353-962509.sp%7CP28130%7CWNT7B_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ98SN7%7CWNT2B_CHICK.for.959547-962572.29.fasta -t /tmp/maker_6B3o0i/29/2284622.959547-962572.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.959547-962572.sp%7CQ98SN7%7CWNT2B_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP51030%7CWNT8C_CHICK.for.960185-962656.29.fasta -t /tmp/maker_6B3o0i/29/2284622.960185-962656.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.960185-962656.sp%7CP51030%7CWNT8C_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ2LMP1%7CWNT3A_CHICK.for.959484-962572.29.fasta -t /tmp/maker_6B3o0i/29/2284622.959484-962572.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.959484-962572.sp%7CQ2LMP1%7CWNT3A_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP28125%7CWNT3A_MELGA.for.961353-962509.29.fasta -t /tmp/maker_6B3o0i/29/2284622.961353-962509.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.961353-962509.sp%7CP28125%7CWNT3A_MELGA.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP28126%7CWNT3B_MELGA.for.961353-962509.29.fasta -t /tmp/maker_6B3o0i/29/2284622.961353-962509.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.961353-962509.sp%7CP28126%7CWNT3B_MELGA.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP49337%7CWNT4_CHICK.for.959496-962572.29.fasta -t /tmp/maker_6B3o0i/29/2284622.959496-962572.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.959496-962572.sp%7CP49337%7CWNT4_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 13
 ...processing 1 of 13
 ...processing 2 of 13
 ...processing 3 of 13
 ...processing 4 of 13
 ...processing 5 of 13
 ...processing 6 of 13
 ...processing 7 of 13
 ...processing 8 of 13
 ...processing 9 of 13
 ...processing 10 of 13
 ...processing 11 of 13
 ...processing 12 of 13
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 11
 ...processing 1 of 11
 ...processing 2 of 11
 ...processing 3 of 11
 ...processing 4 of 11
 ...processing 5 of 11
 ...processing 6 of 11
 ...processing 7 of 11
 ...processing 8 of 11
 ...processing 9 of 11
 ...processing 10 of 11
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
merging blast reports...
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
processing chunk output
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
doing blastx repeats
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/1/2284607.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ5ZKY4%7CING4_CHICK.for.988063-990975.29.fasta -t /tmp/maker_6B3o0i/29/2284622.988063-990975.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.988063-990975.sp%7CQ5ZKY4%7CING4_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
running  blast search.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
collecting blastx reports
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
preparing evidence clusters for annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
processing chunk output
processing all repeats
prepare section files
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CQ2LK54%7CCOL12_CHICK.for.220879-237523.39.fasta -t /tmp/maker_6B3o0i/39/2284485.220879-237523.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.220879-237523.sp%7CQ2LK54%7CCOL12_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1 -pa 1
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284461.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0F/A4/2284461//theVoid.2284461/2/2284461.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
annotating transcripts
Making transcripts
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx repeats
running  blast search.
collecting blastx repeatmasking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing evidence clusters for annotations
processing all repeats
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
collecting blastx repeatmasking
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing the chunk divide
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
processing contig output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP49140%7CSKI_CHICK.for.764902-776580.18.fasta -t /tmp/maker_6B3o0i/18/2284366.764902-776580.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.764902-776580.sp%7CP49140%7CSKI_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284622.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/49/47/2284622//theVoid.2284622/1/2284622.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284788
Length: 1280301
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
choosing best annotation set
Choosing best annotations
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ6JHU8%7CP3H1_CHICK.for.1216696-1226910.29.fasta -t /tmp/maker_6B3o0i/29/2284622.1216696-1226910.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.1216696-1226910.sp%7CQ6JHU8%7CP3H1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CQ6JHU7%7CP3H2_CHICK.for.1215813-1226883.29.fasta -t /tmp/maker_6B3o0i/29/2284622.1215813-1226883.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.1215813-1226883.sp%7CQ6JHU7%7CP3H2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CE1BY77%7CUBP13_CHICK.for.1252958-1266871.29.fasta -t /tmp/maker_6B3o0i/29/2284622.1252958-1266871.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.1252958-1266871.sp%7CE1BY77%7CUBP13_CHICK.p.exonerate
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/29/sp%7CP00940%7CTPIS_CHICK.for.1273520-1275864.29.fasta -t /tmp/maker_6B3o0i/29/2284622.1273520-1275864.29.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/29/2284622.1273520-1275864.sp%7CP00940%7CTPIS_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
merging blast reports...
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
processing the chunk divide
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Preparing evidence for hint based annotation
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
clustering transcripts into genes for annotations
running  blast search.
Processing transcripts into genes
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
processing chunk output
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:29   current j:0
 j_size:29   current j:1
 j_size:29   current j:2
 j_size:29   current j:3
 j_size:29   current j:4
 j_size:29   current j:5
 j_size:29   current j:6
 j_size:29   current j:7
 j_size:29   current j:8
 j_size:29   current j:9
 j_size:29   current j:10
 j_size:29   current j:11
 j_size:29   current j:12
 j_size:29   current j:13
 j_size:29   current j:14
 j_size:29   current j:15
 j_size:29   current j:16
 j_size:29   current j:17
 j_size:29   current j:18
 j_size:29   current j:19
 j_size:29   current j:20
 j_size:29   current j:21
 j_size:29   current j:22
 j_size:29   current j:23
 j_size:29   current j:24
 j_size:29   current j:25
 j_size:29   current j:26
 j_size:29   current j:27
 j_size:29   current j:28
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/0/2284717.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
processing chunk output
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:0 hits
preparing evidence clusters for annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1 -pa 1
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log



--Next Contig--

flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284801
Length: 3406090
#---------------------------------------------------------------------


merging blast reports...
setting up GFF3 output and fasta chunks
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1 -pa 1
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing repeat masking
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/3/2284424.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/3/2284298.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
annotating transcripts
Making transcripts
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ5ZJD8%7CTMM68_CHICK.for.410885-434325.19.fasta -t /tmp/maker_6B3o0i/19/2284644.410885-434325.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284644.410885-434325.sp%7CQ5ZJD8%7CTMM68_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ5ZJD8%7CTMM68_CHICK.for.454290-465809.19.fasta -t /tmp/maker_6B3o0i/19/2284644.454290-465809.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284644.454290-465809.sp%7CQ5ZJD8%7CTMM68_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing chunk output
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/0/2284366.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
adding statistics to annotations
adding statistics to annotations
Calculating annotation quality statistics
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
preparing ab-inits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/0/2284647.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
processing chunk output
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP49140%7CSKI_CHICK.for.923907-925618.18.fasta -t /tmp/maker_6B3o0i/18/2284366.923907-925618.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.923907-925618.sp%7CP49140%7CSKI_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
preparing ab-inits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
deleted:0 hits
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
gathering ab-init output files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
deleted:1 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
collecting blastx reports
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
prepare section files
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284788.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/0/2284722.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
deleted:0 hits
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
collecting blastx reports
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
collecting blastx reports
clustering transcripts into genes for annotations
Processing transcripts into genes
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP18652%7CKS6AA_CHICK.for.833222-845492.7.fasta -t /tmp/maker_6B3o0i/7/2284347.833222-845492.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.833222-845492.sp%7CP18652%7CKS6AA_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
deleted:0 hits
cleaning blastx...
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/4/2283926.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:-1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284801.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 10
 ...processing 1 of 10
 ...processing 2 of 10
 ...processing 3 of 10
 ...processing 4 of 10
 ...processing 5 of 10
 ...processing 6 of 10
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
 ...processing 7 of 10
 ...processing 8 of 10
 ...processing 9 of 10
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing ab-inits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
polishing proteins
adding statistics to annotations
Calculating annotation quality statistics
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ02977%7CYRK_CHICK.for.656046-660253.19.fasta -t /tmp/maker_6B3o0i/19/2284644.656046-660253.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284644.656046-660253.sp%7CQ02977%7CYRK_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP00523%7CSRC_CHICK.for.656046-660253.19.fasta -t /tmp/maker_6B3o0i/19/2284644.656046-660253.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284644.656046-660253.sp%7CP00523%7CSRC_CHICK.p.exonerate
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:27   current j:0
 j_size:27   current j:1
 j_size:27   current j:2
 j_size:27   current j:3
 j_size:27   current j:4
 j_size:27   current j:5
 j_size:27   current j:6
 j_size:27   current j:7
 j_size:27   current j:8
 j_size:27   current j:9
 j_size:27   current j:10
 j_size:27   current j:11
 j_size:27   current j:12
 j_size:27   current j:13
 j_size:27   current j:14
 j_size:27   current j:15
 j_size:27   current j:16
 j_size:27   current j:17
 j_size:27   current j:18
 j_size:27   current j:19
 j_size:27   current j:20
 j_size:27   current j:21
 j_size:27   current j:22
 j_size:27   current j:23
 j_size:27   current j:24
 j_size:27   current j:25
 j_size:27   current j:26
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP42683%7CLCK_CHICK.for.656046-660259.19.fasta -t /tmp/maker_6B3o0i/19/2284644.656046-660259.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284644.656046-660259.sp%7CP42683%7CLCK_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP09324%7CYES_CHICK.for.656046-660253.19.fasta -t /tmp/maker_6B3o0i/19/2284644.656046-660253.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284644.656046-660253.sp%7CP09324%7CYES_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
doing blastx repeats
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/0/2284726.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:6 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
collecting blastx repeatmasking
merging blast reports...
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP24045%7CGBRB4_CHICK.for.1091191-1097420.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1091191-1097420.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1091191-1097420.sp%7CP24045%7CGBRB4_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP19150%7CGBRA1_CHICK.for.1092015-1097420.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1092015-1097420.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1092015-1097420.sp%7CP19150%7CGBRA1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
processing chunk output
collecting blastx reports
collecting blastx reports
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP19019%7CGBRB3_CHICK.for.1091146-1097420.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1091146-1097420.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1091146-1097420.sp%7CP19019%7CGBRB3_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP34904%7CGBRG4_CHICK.for.1091278-1097420.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1091278-1097420.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1091278-1097420.sp%7CP34904%7CGBRG4_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ90845%7CGBRA6_CHICK.for.1091266-1097420.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1091266-1097420.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1091266-1097420.sp%7CQ90845%7CGBRA6_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP21548%7CGBRG2_CHICK.for.1091266-1097420.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1091266-1097420.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1091266-1097420.sp%7CP21548%7CGBRG2_CHICK.p.exonerate
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/1/2284552.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/0/2284347.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
cleaning blastx...
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:9 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1 -pa 1
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:11 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:6 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:6 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:6 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2 -pa 1
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:10 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
deleted:0 hits
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
processing chunk output
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:8 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CP10741%7CMOS_CHICK.for.762077-763923.19.fasta -t /tmp/maker_6B3o0i/19/2284644.762077-763923.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284644.762077-763923.sp%7CP10741%7CMOS_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/19/sp%7CQ58NQ5%7CPLAG1_CHICK.for.776654-779550.19.fasta -t /tmp/maker_6B3o0i/19/2284644.776654-779550.19.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/19/2284644.776654-779550.sp%7CQ58NQ5%7CPLAG1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing contig output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files



--Next Contig--

deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284809
Length: 1313410
#---------------------------------------------------------------------


deleted:0 hits
setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/2/2284530.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284647.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/04/51/2284647//theVoid.2284647/1/2284647.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
choosing best annotation set
Choosing best annotations
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CQ5ZIJ9%7CMIB2_CHICK.for.812814-825203.39.fasta -t /tmp/maker_6B3o0i/39/2284485.812814-825203.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.812814-825203.sp%7CQ5ZIJ9%7CMIB2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
processing all repeats
prepare section files
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 15
 ...processing 1 of 15
 ...processing 2 of 15
 ...processing 3 of 15
 ...processing 4 of 15
 ...processing 5 of 15
 ...processing 6 of 15
 ...processing 7 of 15
 ...processing 8 of 15
 ...processing 9 of 15
flattening protein clusters
 ...processing 10 of 15
 ...processing 11 of 15
 ...processing 12 of 15
 ...processing 13 of 15
 ...processing 14 of 15
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CP79777%7CBRAC_CHICK.for.1046473-1053452.7.fasta -t /tmp/maker_6B3o0i/7/2284347.1046473-1053452.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.1046473-1053452.sp%7CP79777%7CBRAC_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing the chunk divide
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:41   current j:0
 j_size:41   current j:1
 j_size:41   current j:2
 j_size:41   current j:3
 j_size:41   current j:4
 j_size:41   current j:5
 j_size:41   current j:6
 j_size:41   current j:7
 j_size:41   current j:8
 j_size:41   current j:9
 j_size:41   current j:10
 j_size:41   current j:11
 j_size:41   current j:12
 j_size:41   current j:13
 j_size:41   current j:14
 j_size:41   current j:15
 j_size:41   current j:16
 j_size:41   current j:17
 j_size:41   current j:18
 j_size:41   current j:19
 j_size:41   current j:20
 j_size:41   current j:21
 j_size:41   current j:22
 j_size:41   current j:23
 j_size:41   current j:24
 j_size:41   current j:25
 j_size:41   current j:26
 j_size:41   current j:27
 j_size:41   current j:28
 j_size:41   current j:29
 j_size:41   current j:30
 j_size:41   current j:31
 j_size:41   current j:32
 j_size:41   current j:33
 j_size:41   current j:34
 j_size:41   current j:35
 j_size:41   current j:36
 j_size:41   current j:37
 j_size:41   current j:38
 j_size:41   current j:39
 j_size:41   current j:40
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2 -pa 1
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
processing chunk output
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284788.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
preparing evidence clusters for annotations
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
deleted:0 hits
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:1 hits
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing contig output
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
examining contents of the fasta file and run log
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#



--Next Contig--

deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284824
Length: 3085902
#---------------------------------------------------------------------


deleted:0 hits
deleted:1 hits
deleted:0 hits
setting up GFF3 output and fasta chunks
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/0/2284485.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CQ90625%7CZBT17_CHICK.for.64211-66084.14.fasta -t /tmp/maker_6B3o0i/14/2284530.64211-66084.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2284530.64211-66084.sp%7CQ90625%7CZBT17_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
cleaning blastx...
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
cleaning clusters....
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284801.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/0/2284644.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
choosing best annotation set
doing blastx of proteins
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/0/2284436.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CP20678%7CCP2H2_CHICK.for.416548-436058.43.fasta -t /tmp/maker_6B3o0i/43/2284298.416548-436058.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.416548-436058.sp%7CP20678%7CCP2H2_CHICK.p.exonerate
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
polishing proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP13863%7CCDK1_CHICK.for.1418825-1420854.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1418825-1420854.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1418825-1420854.sp%7CP13863%7CCDK1_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
choosing best annotation set
Choosing best annotations
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CP05180%7CCP2H1_CHICK.for.417324-436058.43.fasta -t /tmp/maker_6B3o0i/43/2284298.417324-436058.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.417324-436058.sp%7CP05180%7CCP2H1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
cleaning blastx...
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CQ5ZJ27%7CHOOK1_CHICK.for.450023-477892.43.fasta -t /tmp/maker_6B3o0i/43/2284298.450023-477892.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.450023-477892.sp%7CQ5ZJ27%7CHOOK1_CHICK.p.exonerate
#-------------------------------#
deleted:2 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
collecting blastx reports
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
deleted:0 hits
merging blast reports...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CP43693%7CGATA6_CHICK.for.1020375-1021690.39.fasta -t /tmp/maker_6B3o0i/39/2284485.1020375-1021690.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.1020375-1021690.sp%7CP43693%7CGATA6_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CP43691%7CGATA4_CHICK.for.1020465-1021678.39.fasta -t /tmp/maker_6B3o0i/39/2284485.1020465-1021678.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.1020465-1021678.sp%7CP43691%7CGATA4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CP43692%7CGATA5_CHICK.for.1020375-1021678.39.fasta -t /tmp/maker_6B3o0i/39/2284485.1020375-1021678.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.1020375-1021678.sp%7CP43692%7CGATA5_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CP43693%7CGATA6_CHICK.for.1033011-1047759.39.fasta -t /tmp/maker_6B3o0i/39/2284485.1033011-1047759.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.1033011-1047759.sp%7CP43693%7CGATA6_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CP17678%7CGATA1_CHICK.for.1033014-1037440.39.fasta -t /tmp/maker_6B3o0i/39/2284485.1033014-1037440.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.1033014-1037440.sp%7CP17678%7CGATA1_CHICK.p.exonerate
#-------------------------------#
prepare section files
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CP43691%7CGATA4_CHICK.for.1033014-1038933.39.fasta -t /tmp/maker_6B3o0i/39/2284485.1033014-1038933.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.1033014-1038933.sp%7CP43691%7CGATA4_CHICK.p.exonerate
#-------------------------------#
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/39/sp%7CP43692%7CGATA5_CHICK.for.1033023-1037437.39.fasta -t /tmp/maker_6B3o0i/39/2284485.1033023-1037437.39.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/39/2284485.1033023-1037437.sp%7CP43692%7CGATA5_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
cleaning blastx...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284809.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing repeat masking
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
doing blastx repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1 -pa 1
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
choosing best annotation set
Choosing best annotations
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1 -pa 1
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
collecting blastx repeatmasking
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
adding statistics to annotations
Calculating annotation quality statistics
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
preparing evidence clusters for annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
doing repeat masking
deleted:0 hits
collecting blastx reports
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
prepare section files
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
prepare section files
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284788.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/3/2284120.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
processing chunk output
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
flattening protein clusters
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
collecting blastx reports
merging blast reports...
re-running blast for edge cases...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/18/blastprep/db.1462035-1518516.for_blastx.fasta
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.1462035-1518516.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.1462035.1518516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.1462035.1518516.0.db%2E1462035-1518516%2Efor_blastx%2Efasta.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
...finished
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZIJ9%7CMIB2_CHICK.for.1471635-1508916.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1471635-1508916.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1471635-1508916.sp%7CQ5ZIJ9%7CMIB2_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
running  blast search.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
merging blast reports...
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/0/2284742.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/2/2284616.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284824.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/0/2284744.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
merging blast reports...
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
processing contig output
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
processing contig output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
prepare section files
examining contents of the fasta file and run log
processing all repeats
gathering ab-init output files
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.



--Next Contig--

Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284825
Length: 1603716
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
examining contents of the fasta file and run log
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
doing blastx of proteins
doing repeat masking
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1 -pa 1
#-------------------------------#
doing repeat masking



--Next Contig--

doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284827
Length: 4694515
#---------------------------------------------------------------------


deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
setting up GFF3 output and fasta chunks
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
merging blast reports...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZJQ7%7CSSU72_CHICK.for.1607953-1616815.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1607953-1616815.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1607953-1616815.sp%7CQ5ZJQ7%7CSSU72_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZJQ7%7CSSU72_CHICK.for.1634246-1638231.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1634246-1638231.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1634246-1638231.sp%7CQ5ZJQ7%7CSSU72_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
collecting blastx reports
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284809.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ9YH99%7CEYA3_CHICK.for.588896-589839.34.fasta -t /tmp/maker_6B3o0i/34/2284669.588896-589839.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.588896-589839.sp%7CQ9YH99%7CEYA3_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284801.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
deleted:0 hits
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
doing blastx repeats
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
processing all repeats
in cluster::shadow_cluster...
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:2 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/0/2284752.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/2/2284571.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing repeat masking
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
processing all repeats
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
collecting blastx reports
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
collecting blastx repeatmasking
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
processing all repeats
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing repeat masking
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2 -pa 1
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/3/2284220.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
gathering ab-init output files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1 -pa 1
#-------------------------------#
merging blast reports...
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
in cluster::shadow_cluster...
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284824.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing masked sequence
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/27/sp%7CQ5ZK10%7CNSF1C_CHICK.for.785217-793121.27.fasta -t /tmp/maker_6B3o0i/27/2284424.785217-793121.27.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/27/2284424.785217-793121.sp%7CQ5ZK10%7CNSF1C_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/27/sp%7CQ5ZKI7%7CCB044_CHICK.for.854217-862081.27.fasta -t /tmp/maker_6B3o0i/27/2284424.854217-862081.27.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/27/2284424.854217-862081.sp%7CQ5ZKI7%7CCB044_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284788.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ9YHA0%7CEYA1_CHICK.for.588896-591624.34.fasta -t /tmp/maker_6B3o0i/34/2284669.588896-591624.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.588896-591624.sp%7CQ9YHA0%7CEYA1_CHICK.p.exonerate
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ9YH98%7CEYA4_CHICK.for.588896-591624.34.fasta -t /tmp/maker_6B3o0i/34/2284669.588896-591624.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.588896-591624.sp%7CQ9YH98%7CEYA4_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
doing repeat masking
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
gathering ab-init output files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284825.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CP27921%7CJUND_CHICK.for.876348-877909.43.fasta -t /tmp/maker_6B3o0i/43/2284298.876348-877909.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.876348-877909.sp%7CP27921%7CJUND_CHICK.p.exonerate
#-------------------------------#
prepare section files
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CP18870%7CJUN_CHICK.for.876222-877912.43.fasta -t /tmp/maker_6B3o0i/43/2284298.876222-877912.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.876222-877912.sp%7CP18870%7CJUN_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284827.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2 -pa 1
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZJP9%7CCCNL1_CHICK.for.1807610-1824916.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1807610-1824916.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1807610-1824916.sp%7CQ5ZJP9%7CCCNL1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
flattening protein clusters
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1 -pa 1
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
gathering ab-init output files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx reports
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
doing blastx of proteins
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CQ8UW76%7CTBX20_CHICK.for.9204-19873.35.fasta -t /tmp/maker_6B3o0i/35/2284571.9204-19873.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284571.9204-19873.sp%7CQ8UW76%7CTBX20_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CP79777%7CBRAC_CHICK.for.12218-19873.35.fasta -t /tmp/maker_6B3o0i/35/2284571.12218-19873.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284571.12218-19873.sp%7CP79777%7CBRAC_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CO73718%7CTBX3_CHICK.for.12242-19873.35.fasta -t /tmp/maker_6B3o0i/35/2284571.12242-19873.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284571.12242-19873.sp%7CO73718%7CTBX3_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CQ9PWE8%7CTBX5_CHICK.for.9228-19873.35.fasta -t /tmp/maker_6B3o0i/35/2284571.9228-19873.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284571.9228-19873.sp%7CQ9PWE8%7CTBX5_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CP79779%7CTBX6L_CHICK.for.12188-19873.35.fasta -t /tmp/maker_6B3o0i/35/2284571.12188-19873.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284571.12188-19873.sp%7CP79779%7CTBX6L_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/0/2284424.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
polishing proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/27/sp%7CQ5ZKI7%7CCB044_CHICK.for.897396-900115.27.fasta -t /tmp/maker_6B3o0i/27/2284424.897396-900115.27.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/27/2284424.897396-900115.sp%7CQ5ZKI7%7CCB044_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284809.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/0/2284298.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/1/2284642.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0 -pa 1
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CQ5ZJJ9%7COSTF1_CHICK.for.910581-911647.43.fasta -t /tmp/maker_6B3o0i/43/2284298.910581-911647.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.910581-911647.sp%7CQ5ZJJ9%7COSTF1_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CQ91955%7CMTPN_CHICK.for.909540-911677.43.fasta -t /tmp/maker_6B3o0i/43/2284298.909540-911677.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.909540-911677.sp%7CQ91955%7CMTPN_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CQ5F3F2%7CMYSM1_CHICK.for.914959-930614.43.fasta -t /tmp/maker_6B3o0i/43/2284298.914959-930614.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.914959-930614.sp%7CQ5F3F2%7CMYSM1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/43/sp%7CQ5F381%7CEPCAM_CHICK.for.944625-946333.43.fasta -t /tmp/maker_6B3o0i/43/2284298.944625-946333.43.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/43/2284298.944625-946333.sp%7CQ5F381%7CEPCAM_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
polishing proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/3/sp%7CQ9YH99%7CEYA3_CHICK.for.1466548-1467938.3.fasta -t /tmp/maker_6B3o0i/3/2284436.1466548-1467938.3.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/3/2284436.1466548-1467938.sp%7CQ9YH99%7CEYA3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/3/sp%7CQ9YH98%7CEYA4_CHICK.for.1466548-1468181.3.fasta -t /tmp/maker_6B3o0i/3/2284436.1466548-1468181.3.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/3/2284436.1466548-1468181.sp%7CQ9YH98%7CEYA4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/3/sp%7CQ9YHA0%7CEYA1_CHICK.for.1466548-1468181.3.fasta -t /tmp/maker_6B3o0i/3/2284436.1466548-1468181.3.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/3/2284436.1466548-1468181.sp%7CQ9YHA0%7CEYA1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/1/2284366.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284801.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/11/sp%7CQ90722%7CFGF8_CHICK.for.6188-9286.11.fasta -t /tmp/maker_6B3o0i/11/2284727.6188-9286.11.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/11/2284727.6188-9286.sp%7CQ90722%7CFGF8_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/11/sp%7CQ5ZLT0%7CXPO7_CHICK.for.23103-55015.11.fasta -t /tmp/maker_6B3o0i/11/2284727.23103-55015.11.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/11/2284727.23103-55015.sp%7CQ5ZLT0%7CXPO7_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284644.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/51/7B/2284644//theVoid.2284644/1/2284644.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
cleaning blastx...
collecting blastx reports
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:-2 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
doing blastx of proteins
running  blast search.
polishing proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ90WI4%7CMXRA8_CHICK.for.1880785-1892736.18.fasta -t /tmp/maker_6B3o0i/18/2284366.1880785-1892736.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.1880785-1892736.sp%7CQ90WI4%7CMXRA8_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
flattening protein clusters
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:1 hits
deleted:-2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:19   current j:0
 j_size:19   current j:1
 j_size:19   current j:2
 j_size:19   current j:3
 j_size:19   current j:4
 j_size:19   current j:5
 j_size:19   current j:6
 j_size:19   current j:7
 j_size:19   current j:8
 j_size:19   current j:9
 j_size:19   current j:10
 j_size:19   current j:11
 j_size:19   current j:12
 j_size:19   current j:13
 j_size:19   current j:14
 j_size:19   current j:15
 j_size:19   current j:16
 j_size:19   current j:17
 j_size:19   current j:18
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/4/2283486.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
prepare section files
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
flattening protein clusters
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing masked sequence
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:3 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0 -pa 1
#-------------------------------#
deleted:0 hits
flattening protein clusters
collecting blastx reports
merging blast reports...
prepare section files
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
processing the chunk divide
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
doing repeat masking
doing repeat masking
Preparing evidence for hint based annotation
merging blast reports...
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4 -pa 1
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/0/2284760.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/27/sp%7CQ07883%7CGRB2_CHICK.for.1066171-1067135.27.fasta -t /tmp/maker_6B3o0i/27/2284424.1066171-1067135.27.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/27/2284424.1066171-1067135.sp%7CQ07883%7CGRB2_CHICK.p.exonerate
#-------------------------------#
prepare section files
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/27/sp%7CQ5ZJJ9%7COSTF1_CHICK.for.1066165-1067126.27.fasta -t /tmp/maker_6B3o0i/27/2284424.1066165-1067126.27.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/27/2284424.1066165-1067126.sp%7CQ5ZJJ9%7COSTF1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01014%7COVALY_CHICK.for.843782-868985.4.fasta -t /tmp/maker_6B3o0i/4/2283926.843782-868985.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.843782-868985.sp%7CP01014%7COVALY_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73790%7CSPB10_CHICK.for.843782-871788.4.fasta -t /tmp/maker_6B3o0i/4/2283926.843782-871788.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.843782-871788.sp%7CO73790%7CSPB10_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01012%7COVAL_CHICK.for.843782-868985.4.fasta -t /tmp/maker_6B3o0i/4/2283926.843782-868985.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.843782-868985.sp%7CP01012%7COVAL_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CQ90935%7CNEUS_CHICK.for.843782-854464.4.fasta -t /tmp/maker_6B3o0i/4/2283926.843782-854464.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.843782-854464.sp%7CQ90935%7CNEUS_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73860%7COVAL_MELGA.for.843782-865280.4.fasta -t /tmp/maker_6B3o0i/4/2283926.843782-865280.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.843782-865280.sp%7CO73860%7COVAL_MELGA.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01013%7COVALX_CHICK.for.843782-868982.4.fasta -t /tmp/maker_6B3o0i/4/2283926.843782-868982.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.843782-868982.sp%7CP01013%7COVALX_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2 -pa 1
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
flattening protein clusters
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP13731%7CSERPH_CHICK.for.843782-854464.4.fasta -t /tmp/maker_6B3o0i/4/2283926.843782-854464.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.843782-854464.sp%7CP13731%7CSERPH_CHICK.p.exonerate
#-------------------------------#
deleted:4 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 5 of 7
 ...processing 6 of 7
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
prepare section files
collecting blastx repeatmasking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:-1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284788.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284824.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-3 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4 -pa 1
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-3 hits
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/11/sp%7CO13157%7CGFRA2_CHICK.for.126854-138571.11.fasta -t /tmp/maker_6B3o0i/11/2284727.126854-138571.11.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/11/2284727.126854-138571.sp%7CO13157%7CGFRA2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/11/sp%7CO93512%7CGFRA4_CHICK.for.137203-138571.11.fasta -t /tmp/maker_6B3o0i/11/2284727.137203-138571.11.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/11/2284727.137203-138571.sp%7CO93512%7CGFRA4_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/11/sp%7CO13157%7CGFRA2_CHICK.for.148227-150985.11.fasta -t /tmp/maker_6B3o0i/11/2284727.148227-150985.11.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/11/2284727.148227-150985.sp%7CO13157%7CGFRA2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0 -pa 1
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
collecting blastx reports
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
prepare section files
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CP49147%7CPA24A_CHICK.for.217994-225725.13.fasta -t /tmp/maker_6B3o0i/13/2284676.217994-225725.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.217994-225725.sp%7CP49147%7CPA24A_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
cleaning blastx...
deleted:0 hits
doing blastx repeats
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZIH0%7CINT11_CHICK.for.2062186-2074042.18.fasta -t /tmp/maker_6B3o0i/18/2284366.2062186-2074042.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.2062186-2074042.sp%7CQ5ZIH0%7CINT11_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2 -pa 1
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
collecting blastx reports
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/0/2284669.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284825.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284827.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
doing blastx repeats
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
re-running blast for edge cases...
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/4/blastprep/db.884639-910758.for_blastx.fasta
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.884639-910758.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.884639.910758.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/0/2283926.884639.910758.0.db%2E884639-910758%2Efor_blastx%2Efasta.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
...finished
collecting blastx repeatmasking
prepare section files
collecting blastx reports
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx of proteins
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CO93603%7CTRFR_CHICK.for.917376-927192.34.fasta -t /tmp/maker_6B3o0i/34/2284669.917376-927192.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.917376-927192.sp%7CO93603%7CTRFR_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73860%7COVAL_MELGA.for.894239-897970.4.fasta -t /tmp/maker_6B3o0i/4/2283926.894239-897970.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.894239-897970.sp%7CO73860%7COVAL_MELGA.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73790%7CSPB10_CHICK.for.894239-901158.4.fasta -t /tmp/maker_6B3o0i/4/2283926.894239-901158.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.894239-901158.sp%7CO73790%7CSPB10_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01014%7COVALY_CHICK.for.894239-901158.4.fasta -t /tmp/maker_6B3o0i/4/2283926.894239-901158.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.894239-901158.sp%7CP01014%7COVALY_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01014%7COVALY_CHICK.for.915742-921692.4.fasta -t /tmp/maker_6B3o0i/4/2283926.915742-921692.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.915742-921692.sp%7CP01014%7COVALY_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73790%7CSPB10_CHICK.for.915742-921692.4.fasta -t /tmp/maker_6B3o0i/4/2283926.915742-921692.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.915742-921692.sp%7CO73790%7CSPB10_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01013%7COVALX_CHICK.for.914685-917408.4.fasta -t /tmp/maker_6B3o0i/4/2283926.914685-917408.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.914685-917408.sp%7CP01013%7COVALX_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01014%7COVALY_CHICK.for.939284-945620.4.fasta -t /tmp/maker_6B3o0i/4/2283926.939284-945620.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.939284-945620.sp%7CP01014%7COVALY_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01012%7COVAL_CHICK.for.939284-945620.4.fasta -t /tmp/maker_6B3o0i/4/2283926.939284-945620.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.939284-945620.sp%7CP01012%7COVAL_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73860%7COVAL_MELGA.for.939284-945620.4.fasta -t /tmp/maker_6B3o0i/4/2283926.939284-945620.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.939284-945620.sp%7CO73860%7COVAL_MELGA.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01013%7COVALX_CHICK.for.939284-942017.4.fasta -t /tmp/maker_6B3o0i/4/2283926.939284-942017.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.939284-942017.sp%7CP01013%7COVALX_CHICK.p.exonerate
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01013%7COVALX_CHICK.for.966152-977519.4.fasta -t /tmp/maker_6B3o0i/4/2283926.966152-977519.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.966152-977519.sp%7CP01013%7COVALX_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 ...processing 3 of 4
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:4 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/0/2284753.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
collecting blastx repeatmasking
collecting blastx reports
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1 -pa 1
#-------------------------------#
flattening protein clusters
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284809.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/1/2284347.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing all repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing chunk output
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0 -pa 1
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:-1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
flattening protein clusters
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/10/sp%7CQ5ZIG0%7CNCDN_CHICK.for.122827-126597.10.fasta -t /tmp/maker_6B3o0i/10/2284707.122827-126597.10.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/10/2284707.122827-126597.sp%7CQ5ZIG0%7CNCDN_CHICK.p.exonerate
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
merging blast reports...
doing blastx repeats
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
collecting blastx reports
merging blast reports...
deleted:0 hits
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
flattening protein clusters
collecting blastx reports
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
merging blast reports...
re-running blast for edge cases...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/4/blastprep/db.956552-1018014.for_blastx.fasta
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.956552-1018014.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.956552.1018014.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.956552.1018014.0.db%2E956552-1018014%2Efor_blastx%2Efasta.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ98ST5%7CCRLD1_CHICK.for.1061885-1066572.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1061885-1066572.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1061885-1066572.sp%7CQ98ST5%7CCRLD1_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ98ST6%7CPI15_CHICK.for.1061921-1066605.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1061921-1066605.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1061921-1066605.sp%7CQ98ST6%7CPI15_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
cleaning blastx...
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing repeat masking
prepare section files
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01013%7COVALX_CHICK.for.1002843-1005263.4.fasta -t /tmp/maker_6B3o0i/4/2283926.1002843-1005263.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.1002843-1005263.sp%7CP01013%7COVALX_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01013%7COVALX_CHICK.for.988320-991192.4.fasta -t /tmp/maker_6B3o0i/4/2283926.988320-991192.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.988320-991192.sp%7CP01013%7COVALX_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CQ90935%7CNEUS_CHICK.for.1002843-1004008.4.fasta -t /tmp/maker_6B3o0i/4/2283926.1002843-1004008.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.1002843-1004008.sp%7CQ90935%7CNEUS_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01014%7COVALY_CHICK.for.966152-1008414.4.fasta -t /tmp/maker_6B3o0i/4/2283926.966152-1008414.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.966152-1008414.sp%7CP01014%7COVALY_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01012%7COVAL_CHICK.for.966152-1008414.4.fasta -t /tmp/maker_6B3o0i/4/2283926.966152-1008414.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.966152-1008414.sp%7CP01012%7COVAL_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73860%7COVAL_MELGA.for.966152-1008414.4.fasta -t /tmp/maker_6B3o0i/4/2283926.966152-1008414.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.966152-1008414.sp%7CO73860%7COVAL_MELGA.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73790%7CSPB10_CHICK.for.966152-1008414.4.fasta -t /tmp/maker_6B3o0i/4/2283926.966152-1008414.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.966152-1008414.sp%7CO73790%7CSPB10_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CP01014%7COVALY_CHICK.for.1024565-1032526.4.fasta -t /tmp/maker_6B3o0i/4/2283926.1024565-1032526.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.1024565-1032526.sp%7CP01014%7COVALY_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73790%7CSPB10_CHICK.for.1024565-1032526.4.fasta -t /tmp/maker_6B3o0i/4/2283926.1024565-1032526.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.1024565-1032526.sp%7CO73790%7CSPB10_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CO73790%7CSPB10_CHICK.for.1042533-1045243.4.fasta -t /tmp/maker_6B3o0i/4/2283926.1042533-1045243.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.1042533-1045243.sp%7CO73790%7CSPB10_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
 ...processing 3 of 6
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
 ...processing 4 of 6
 ...processing 5 of 6
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 10
 ...processing 1 of 10
 ...processing 2 of 10
 ...processing 3 of 10
 ...processing 4 of 10
 ...processing 5 of 10
 ...processing 6 of 10
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
 ...processing 7 of 10
 ...processing 8 of 10
 ...processing 9 of 10
total clusters:2 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/2/2284509.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:18 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx of proteins
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 2
 ...processing 1 of 2
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
collecting blastx repeatmasking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
flattening protein clusters
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284824.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
collecting blastx reports
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
adding statistics to annotations
Calculating annotation quality statistics
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
prepare section files
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
prepare section files
deleted:1 hits
deleted:0 hits
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:11 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/0/2284765.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
processing chunk output
doing blastx repeats
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
doing blastx of proteins
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/0/2284530.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:10 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1 -pa 1
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
merging blast reports...
collecting blastx repeatmasking
re-running blast for edge cases...
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/18/blastprep/db.2187926-2220528.for_blastx.fasta
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.2187926-2220528.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.2187926.2220528.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.2187926.2220528.0.db%2E2187926-2220528%2Efor_blastx%2Efasta.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
...finished
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
deleted:0 hits
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing chunk output
deleted:9 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4 -pa 1
#-------------------------------#
polishing proteins
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZK62%7CACAP2_CHICK.for.2197526-2210928.18.fasta -t /tmp/maker_6B3o0i/18/2284366.2197526-2210928.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.2197526-2210928.sp%7CQ5ZK62%7CACAP2_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ92075%7CSCNNA_CHICK.for.2224819-2235327.18.fasta -t /tmp/maker_6B3o0i/18/2284366.2224819-2235327.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.2224819-2235327.sp%7CQ92075%7CSCNNA_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
cleaning blastx...
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284801.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
doing blastx repeats
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
flattening protein clusters
collecting blastx reports
doing blastx of proteins
doing repeat masking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284788.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/10/sp%7CQ5ZK88%7CPSPC1_CHICK.for.259358-262503.10.fasta -t /tmp/maker_6B3o0i/10/2284707.259358-262503.10.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/10/2284707.259358-262503.sp%7CQ5ZK88%7CPSPC1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
cleaning blastx...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:1 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/1/2284485.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
polishing proteins
doing blastx of proteins
doing blastx repeats
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CQ07816%7CB2CL1_CHICK.for.1161911-1163286.4.fasta -t /tmp/maker_6B3o0i/4/2283926.1161911-1163286.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.1161911-1163286.sp%7CQ07816%7CB2CL1_CHICK.p.exonerate
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:9   current j:0
 j_size:9   current j:1
 j_size:9   current j:2
 j_size:9   current j:3
 j_size:9   current j:4
 j_size:9   current j:5
 j_size:9   current j:6
 j_size:9   current j:7
 j_size:9   current j:8
...finished clustering.
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/4/sp%7CQ00709%7CBCL2_CHICK.for.1161881-1163280.4.fasta -t /tmp/maker_6B3o0i/4/2283926.1161881-1163280.4.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/4/2283926.1161881-1163280.sp%7CQ00709%7CBCL2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
cleaning blastx...
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/0/2284776.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:13 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
running  blast search.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
re-running blast for edge cases...
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/34/blastprep/db.1082946-1114921.for_blastx.fasta
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.1082946-1114921.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.1082946.1114921.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.1082946.1114921.0.db%2E1082946-1114921%2Efor_blastx%2Efasta.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
...finished
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx reports
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/5/2283486.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ90733%7CCOT2_CHICK.for.1092546-1105321.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1092546-1105321.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1092546-1105321.sp%7CQ90733%7CCOT2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ5ZKP6%7CADA_CHICK.for.1179742-1190102.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1179742-1190102.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1179742-1190102.sp%7CQ5ZKP6%7CADA_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
cleaning blastx...
deleted:6 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1 -pa 1
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:8 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing masked sequence
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx repeatmasking
merging blast reports...
doing blastx repeats
deleted:3 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:11 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:3 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/11/sp%7CP49712%7CVATB_CHICK.for.462747-467388.11.fasta -t /tmp/maker_6B3o0i/11/2284727.462747-467388.11.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/11/2284727.462747-467388.sp%7CP49712%7CVATB_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
polishing proteins
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ92178%7CCAN2_CHICK.for.486145-495354.13.fasta -t /tmp/maker_6B3o0i/13/2284676.486145-495354.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.486145-495354.sp%7CQ92178%7CCAN2_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CP00789%7CCANX_CHICK.for.486145-495348.13.fasta -t /tmp/maker_6B3o0i/13/2284676.486145-495348.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.486145-495348.sp%7CP00789%7CCANX_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CQ92177%7CCAN3_CHICK.for.483371-495369.13.fasta -t /tmp/maker_6B3o0i/13/2284676.483371-495369.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.483371-495369.sp%7CQ92177%7CCAN3_CHICK.p.exonerate
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CP60878%7CSNP25_CHICK.for.578233-583486.13.fasta -t /tmp/maker_6B3o0i/13/2284676.578233-583486.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.578233-583486.sp%7CP60878%7CSNP25_CHICK.p.exonerate
#-------------------------------#
deleted:1 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
cleaning blastx...
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
deleted:0 hits
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
gathering ab-init output files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284827.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
merging blast reports...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284825.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:11 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx repeats
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
doing blastx of proteins
doing blastx of proteins
deleted:0 hits
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/10/sp%7CP36381%7CCXA8_CHICK.for.327086-348179.10.fasta -t /tmp/maker_6B3o0i/10/2284707.327086-348179.10.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/10/2284707.327086-348179.sp%7CP36381%7CCXA8_CHICK.p.exonerate
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/10/sp%7CO93533%7CCXB6_CHICK.for.327239-348182.10.fasta -t /tmp/maker_6B3o0i/10/2284707.327239-348182.10.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/10/2284707.327239-348182.sp%7CO93533%7CCXB6_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/10/sp%7CP14154%7CCXA1_CHICK.for.327026-348179.10.fasta -t /tmp/maker_6B3o0i/10/2284707.327026-348179.10.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/10/2284707.327026-348179.sp%7CP14154%7CCXA1_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/10/sp%7CP29415%7CCXA3_CHICK.for.327266-348179.10.fasta -t /tmp/maker_6B3o0i/10/2284707.327266-348179.10.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/10/2284707.327266-348179.sp%7CP29415%7CCXA3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:3 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/10/sp%7CP18860%7CCXA5_CHICK.for.327053-348179.10.fasta -t /tmp/maker_6B3o0i/10/2284707.327053-348179.10.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/10/2284707.327053-348179.sp%7CP18860%7CCXA5_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
cleaning blastx...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing repeat masking
merging blast reports...
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/1/2284700.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284809.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/1/2284436.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
prepare section files
deleted:0 hits
collecting blastx repeatmasking
collecting blastx reports
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
flattening protein clusters
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/0/2284777.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:18   current j:0
 j_size:18   current j:1
 j_size:18   current j:2
 j_size:18   current j:3
 j_size:18   current j:4
 j_size:18   current j:5
 j_size:18   current j:6
 j_size:18   current j:7
 j_size:18   current j:8
 j_size:18   current j:9
 j_size:18   current j:10
 j_size:18   current j:11
 j_size:18   current j:12
 j_size:18   current j:13
 j_size:18   current j:14
 j_size:18   current j:15
 j_size:18   current j:16
 j_size:18   current j:17
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:2 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0 -pa 1
#-------------------------------#
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CP28686%7CNOV_CHICK.for.1230086-1232336.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1230086-1232336.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1230086-1232336.sp%7CP28686%7CNOV_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CP19336%7CCYR61_CHICK.for.1230098-1232336.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1230098-1232336.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1230098-1232336.sp%7CP19336%7CCYR61_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
preparing masked sequence
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
preparing ab-inits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
prepare section files
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
gathering ab-init output files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:8   current j:0
 j_size:8   current j:1
 j_size:8   current j:2
 j_size:8   current j:3
 j_size:8   current j:4
 j_size:8   current j:5
 j_size:8   current j:6
 j_size:8   current j:7
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
processing chunk output
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/11/sp%7CP0C597%7CDUPD1_CHICK.for.529464-531112.11.fasta -t /tmp/maker_6B3o0i/11/2284727.529464-531112.11.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/11/2284727.529464-531112.sp%7CP0C597%7CDUPD1_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
processing contig output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ5ZKE5%7CCAB45_CHICK.for.2401003-2416994.18.fasta -t /tmp/maker_6B3o0i/18/2284366.2401003-2416994.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.2401003-2416994.sp%7CQ5ZKE5%7CCAB45_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
examining contents of the fasta file and run log



--Next Contig--

deleted:0 hits
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: 2284828
Length: 3306726
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
flattening protein clusters
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/1/2284673.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:3 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
processing all repeats
in cluster::shadow_cluster...
doing blastx repeats
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4 -pa 1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
collecting blastx repeatmasking
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284824.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:6   current j:0
 j_size:6   current j:1
 j_size:6   current j:2
 j_size:6   current j:3
 j_size:6   current j:4
 j_size:6   current j:5
...finished clustering.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2 -pa 1
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
prepare section files
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
flattening protein clusters
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/0/2284616.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
flattening protein clusters
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP18943%7CCOX1_CHICK.for.2504112-2505815.18.fasta -t /tmp/maker_6B3o0i/18/2284366.2504112-2505815.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.2504112-2505815.sp%7CP18943%7CCOX1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
cleaning blastx...
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284788.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
prepare section files
doing blastx of proteins
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
collecting blastx reports
doing blastx of proteins
doing blastx repeats
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
doing repeat masking
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:23   current j:0
 j_size:23   current j:1
 j_size:23   current j:2
 j_size:23   current j:3
 j_size:23   current j:4
 j_size:23   current j:5
 j_size:23   current j:6
 j_size:23   current j:7
 j_size:23   current j:8
 j_size:23   current j:9
 j_size:23   current j:10
 j_size:23   current j:11
 j_size:23   current j:12
 j_size:23   current j:13
 j_size:23   current j:14
 j_size:23   current j:15
 j_size:23   current j:16
 j_size:23   current j:17
 j_size:23   current j:18
 j_size:23   current j:19
 j_size:23   current j:20
 j_size:23   current j:21
 j_size:23   current j:22
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx repeats
doing blastx repeats
flattening protein clusters
doing blastx of proteins
running  blast search.
running  blast search.
collecting blastx reports
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
processing all repeats
doing blastx repeats
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
running  repeat masker.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1 -pa 1
#-------------------------------#
merging blast reports...
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:5   current j:0
 j_size:5   current j:1
 j_size:5   current j:2
 j_size:5   current j:3
 j_size:5   current j:4
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:1 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:-1 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
deleted:0 hits
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
doing blastx of proteins
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx of proteins
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284801.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/8/sp%7CQ58NQ4%7CFOXP1_CHICK.for.147750-170596.8.fasta -t /tmp/maker_6B3o0i/8/2284700.147750-170596.8.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/8/2284700.147750-170596.sp%7CQ58NQ4%7CFOXP1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ5F3W6%7C1433G_CHICK.for.1394057-1398959.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1394057-1398959.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1394057-1398959.sp%7CQ5F3W6%7C1433G_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ5ZMT0%7C1433E_CHICK.for.1394060-1398944.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1394060-1398944.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1394060-1398944.sp%7CQ5ZMT0%7C1433E_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ5ZMD1%7C1433T_CHICK.for.1394057-1398974.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1394057-1398974.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1394057-1398974.sp%7CQ5ZMD1%7C1433T_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ5ZLQ6%7C1433B_CHICK.for.1394057-1398944.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1394057-1398944.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1394057-1398944.sp%7CQ5ZLQ6%7C1433B_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ5ZKC9%7C1433Z_CHICK.for.1394057-1398944.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1394057-1398944.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1394057-1398944.sp%7CQ5ZKC9%7C1433Z_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ5ZJK4%7CSTK4_CHICK.for.1435465-1445229.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1435465-1445229.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1435465-1445229.sp%7CQ5ZJK4%7CSTK4_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
doing blastx of proteins
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 5
 ...processing 1 of 5
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
total clusters:2 now processing 0
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/3/sp%7CO73606%7CKCNG2_CHICK.for.2137476-2138758.3.fasta -t /tmp/maker_6B3o0i/3/2284436.2137476-2138758.3.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/3/2284436.2137476-2138758.sp%7CO73606%7CKCNG2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
cleaning blastx...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
flattening protein clusters
collecting blastx reports
prepare section files
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
collecting blastx reports
prepare section files
deleted:0 hits
merging blast reports...
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
deleted:0 hits
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
flattening protein clusters
collecting blastx reports
flattening protein clusters
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284827.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
merging blast reports...
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284825.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
prepare section files
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
prepare section files
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/39/2284485.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/48/46/2284485//theVoid.2284485/2/2284485.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:2 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
doing blastx of proteins
running  blast search.
in cluster::shadow_cluster...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:2 hits
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:1 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing repeat masking
deleted:0 hits
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0 -pa 1
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1 -pa 1
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:20   current j:0
 j_size:20   current j:1
 j_size:20   current j:2
 j_size:20   current j:3
 j_size:20   current j:4
 j_size:20   current j:5
 j_size:20   current j:6
 j_size:20   current j:7
 j_size:20   current j:8
 j_size:20   current j:9
 j_size:20   current j:10
 j_size:20   current j:11
 j_size:20   current j:12
 j_size:20   current j:13
 j_size:20   current j:14
 j_size:20   current j:15
 j_size:20   current j:16
 j_size:20   current j:17
 j_size:20   current j:18
 j_size:20   current j:19
...finished clustering.
processing the chunk divide
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
doing repeat masking
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/2/2284607.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284809.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
doing blastx of proteins
prepare section files
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
merging blast reports...
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/34/2284669.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/96/7F/2284669//theVoid.2284669/1/2284669.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
flattening protein clusters
deleted:0 hits
flattening protein clusters
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
collecting blastx repeatmasking
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/0/2284676.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  blast search.
processing chunk output
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
prepare section files
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
prepare section files
merging blast reports...
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing evidence clusters for annotations
collecting blastx reports
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing repeat masking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0 -pa 1
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/0/2284571.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:15   current j:0
 j_size:15   current j:1
 j_size:15   current j:2
 j_size:15   current j:3
 j_size:15   current j:4
 j_size:15   current j:5
 j_size:15   current j:6
 j_size:15   current j:7
 j_size:15   current j:8
 j_size:15   current j:9
 j_size:15   current j:10
 j_size:15   current j:11
 j_size:15   current j:12
 j_size:15   current j:13
 j_size:15   current j:14
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CQ7T199%7CKCA10_CHICK.for.1510603-1518743.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1510603-1518743.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1510603-1518743.sp%7CQ7T199%7CKCA10_CHICK.p.exonerate
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
merging blast reports...
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CO73606%7CKCNG2_CHICK.for.1510588-1518743.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1510588-1518743.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1510588-1518743.sp%7CO73606%7CKCNG2_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CP05099%7CMATN1_CHICK.for.1545228-1550443.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1545228-1550443.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1545228-1550443.sp%7CP05099%7CMATN1_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CO42401%7CMATN3_CHICK.for.1545775-1550443.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1545775-1550443.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1545775-1550443.sp%7CO42401%7CMATN3_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/34/sp%7CP49416%7CSDC4_CHICK.for.1599631-1609600.34.fasta -t /tmp/maker_6B3o0i/34/2284669.1599631-1609600.34.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/34/2284669.1599631-1609600.sp%7CP49416%7CSDC4_CHICK.p.exonerate
#-------------------------------#
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1 -pa 1
#-------------------------------#
deleted:0 hits
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
doing blastx of proteins
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
merging blast reports...
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
collecting blastx reports
choosing best annotation set
Choosing best annotations
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/35/sp%7CP40927%7CMAOX_COLLI.for.926216-941902.35.fasta -t /tmp/maker_6B3o0i/35/2284571.926216-941902.35.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/35/2284571.926216-941902.sp%7CP40927%7CMAOX_COLLI.p.exonerate
#-------------------------------#
prepare section files
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/41/2284722.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
deleted:0 hits
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284828.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
prepare section files
deleted:0 hits
flattening protein clusters
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing masked sequence
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1 -pa 1
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CQ90687%7CPTN11_CHICK.for.2714146-2735618.18.fasta -t /tmp/maker_6B3o0i/18/2284366.2714146-2735618.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.2714146-2735618.sp%7CQ90687%7CPTN11_CHICK.p.exonerate
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/9/2284744.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
cleaning blastx...
deleted:0 hits
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
preparing ab-inits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing the chunk divide
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
gathering ab-init output files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/23/2284552.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:4   current j:0
 j_size:4   current j:1
 j_size:4   current j:2
 j_size:4   current j:3
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:26   current j:0
 j_size:26   current j:1
 j_size:26   current j:2
 j_size:26   current j:3
 j_size:26   current j:4
 j_size:26   current j:5
 j_size:26   current j:6
 j_size:26   current j:7
 j_size:26   current j:8
 j_size:26   current j:9
 j_size:26   current j:10
 j_size:26   current j:11
 j_size:26   current j:12
 j_size:26   current j:13
 j_size:26   current j:14
 j_size:26   current j:15
 j_size:26   current j:16
 j_size:26   current j:17
 j_size:26   current j:18
 j_size:26   current j:19
 j_size:26   current j:20
 j_size:26   current j:21
 j_size:26   current j:22
 j_size:26   current j:23
 j_size:26   current j:24
 j_size:26   current j:25
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1 -pa 1
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:25   current j:0
 j_size:25   current j:1
 j_size:25   current j:2
 j_size:25   current j:3
 j_size:25   current j:4
 j_size:25   current j:5
 j_size:25   current j:6
 j_size:25   current j:7
 j_size:25   current j:8
 j_size:25   current j:9
 j_size:25   current j:10
 j_size:25   current j:11
 j_size:25   current j:12
 j_size:25   current j:13
 j_size:25   current j:14
 j_size:25   current j:15
 j_size:25   current j:16
 j_size:25   current j:17
 j_size:25   current j:18
 j_size:25   current j:19
 j_size:25   current j:20
 j_size:25   current j:21
 j_size:25   current j:22
 j_size:25   current j:23
 j_size:25   current j:24
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
adding statistics to annotations
Calculating annotation quality statistics
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/12/2284673.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:22   current j:0
 j_size:22   current j:1
 j_size:22   current j:2
 j_size:22   current j:3
 j_size:22   current j:4
 j_size:22   current j:5
 j_size:22   current j:6
 j_size:22   current j:7
 j_size:22   current j:8
 j_size:22   current j:9
 j_size:22   current j:10
 j_size:22   current j:11
 j_size:22   current j:12
 j_size:22   current j:13
 j_size:22   current j:14
 j_size:22   current j:15
 j_size:22   current j:16
 j_size:22   current j:17
 j_size:22   current j:18
 j_size:22   current j:19
 j_size:22   current j:20
 j_size:22   current j:21
...finished clustering.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.25.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2 -pa 1
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.23.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.3.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/3/sp%7CQ7T199%7CKCA10_CHICK.for.2348805-2350279.3.fasta -t /tmp/maker_6B3o0i/3/2284436.2348805-2350279.3.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/3/2284436.2348805-2350279.sp%7CQ7T199%7CKCA10_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.15.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing chunk output
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/40/2284824.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
doing blastx of proteins
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/6/2284509.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
prepare section files
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/0/2284727.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/1/2284424.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
prepare section files
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:28   current j:0
 j_size:28   current j:1
 j_size:28   current j:2
 j_size:28   current j:3
 j_size:28   current j:4
 j_size:28   current j:5
 j_size:28   current j:6
 j_size:28   current j:7
 j_size:28   current j:8
 j_size:28   current j:9
 j_size:28   current j:10
 j_size:28   current j:11
 j_size:28   current j:12
 j_size:28   current j:13
 j_size:28   current j:14
 j_size:28   current j:15
 j_size:28   current j:16
 j_size:28   current j:17
 j_size:28   current j:18
 j_size:28   current j:19
 j_size:28   current j:20
 j_size:28   current j:21
 j_size:28   current j:22
 j_size:28   current j:23
 j_size:28   current j:24
 j_size:28   current j:25
 j_size:28   current j:26
 j_size:28   current j:27
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
polishing proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CO42282%7CRDS2_CHICK.for.990791-992202.13.fasta -t /tmp/maker_6B3o0i/13/2284676.990791-992202.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.990791-992202.sp%7CO42282%7CRDS2_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CO42281%7CPRPH2_CHICK.for.990791-992166.13.fasta -t /tmp/maker_6B3o0i/13/2284676.990791-992166.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.990791-992166.sp%7CO42281%7CPRPH2_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CO42282%7CRDS2_CHICK.for.1005294-1008081.13.fasta -t /tmp/maker_6B3o0i/13/2284676.1005294-1008081.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.1005294-1008081.sp%7CO42282%7CRDS2_CHICK.p.exonerate
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CP18359%7CDEST_CHICK.for.1210475-1211960.28.fasta -t /tmp/maker_6B3o0i/28/2284616.1210475-1211960.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2284616.1210475-1211960.sp%7CP18359%7CDEST_CHICK.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/28/sp%7CP21566%7CCOF2_CHICK.for.1210475-1211960.28.fasta -t /tmp/maker_6B3o0i/28/2284616.1210475-1211960.28.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/28/2284616.1210475-1211960.sp%7CP21566%7CCOF2_CHICK.p.exonerate
#-------------------------------#
cleaning blastx...
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/13/sp%7CO42281%7CPRPH2_CHICK.for.1005294-1007985.13.fasta -t /tmp/maker_6B3o0i/13/2284676.1005294-1007985.13.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/13/2284676.1005294-1007985.sp%7CO42281%7CPRPH2_CHICK.p.exonerate
#-------------------------------#
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.0.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing repeat masking
doing blastx of proteins
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3 -pa 1
#-------------------------------#
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx reports
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
processing chunk output
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
collecting blastx reports
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
merging blast reports...
re-running blast for edge cases...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
formating database...
#--------- command -------------#
Widget::formater:
/apps/group/bioinformatics/apps/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_6B3o0i/18/blastprep/db.2777776-2841891.for_blastx.fasta
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/db.2777776-2841891.for_blastx.fasta -query /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.2777776.2841891.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.2777776.2841891.0.db%2E2777776-2841891%2Efor_blastx%2Efasta.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
deleted:0 hits
...finished
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/21/2284726.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/20/2284776.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CP31696%7CAGRIN_CHICK.for.2787376-2832291.18.fasta -t /tmp/maker_6B3o0i/18/2284366.2787376-2832291.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.2787376-2832291.sp%7CP31696%7CAGRIN_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
deleted:0 hits
cleaning blastx...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
cleaning clusters....
total clusters:1 now processing 0
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
cleaning clusters....
total clusters:1 now processing 0
collecting blastx repeatmasking
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
clustering transcripts into genes for annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/17/2284642.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:-1 hits
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
 sorting hits in shadow cluster...
 j_size:16   current j:0
 j_size:16   current j:1
 j_size:16   current j:2
 j_size:16   current j:3
 j_size:16   current j:4
 j_size:16   current j:5
 j_size:16   current j:6
 j_size:16   current j:7
 j_size:16   current j:8
 j_size:16   current j:9
 j_size:16   current j:10
 j_size:16   current j:11
 j_size:16   current j:12
 j_size:16   current j:13
 j_size:16   current j:14
 j_size:16   current j:15
...finished clustering.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
processing all repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
clustering transcripts into genes for annotations
Processing transcripts into genes
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.8.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.16.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
processing chunk output
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.27.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
flattening protein clusters
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.23.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
deleted:0 hits
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/33/2284220.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/1/2284298.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/37/2284765.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/7/sp%7CQ9YH18%7CQKI_CHICK.for.2710743-2717026.7.fasta -t /tmp/maker_6B3o0i/7/2284347.2710743-2717026.7.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/7/2284347.2710743-2717026.sp%7CQ9YH18%7CQKI_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
cleaning blastx...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.44.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4 -pa 1
#-------------------------------#
deleted:2 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
flattening protein clusters
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.24.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.4.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/15/2284788.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/38/2284717.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
flattening protein clusters
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx reports
prepare section files
doing blastx of proteins
collecting blastx reports
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.16.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
merging blast reports...
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
flattening protein clusters
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CP00174%7CCYB5_CHICK.for.1602714-1603708.14.fasta -t /tmp/maker_6B3o0i/14/2284530.1602714-1603708.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2284530.1602714-1603708.sp%7CP00174%7CCYB5_CHICK.p.exonerate
#-------------------------------#
deleted:0 hits
prepare section files
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/14/sp%7CP00174%7CCYB5_CHICK.for.1613924-1614855.14.fasta -t /tmp/maker_6B3o0i/14/2284530.1613924-1614855.14.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/14/2284530.1613924-1614855.sp%7CP00174%7CCYB5_CHICK.p.exonerate
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning blastx...
deleted:0 hits
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx reports
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/25/2284801.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.8.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
merging blast reports...
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.1.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1/2284717.18.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B9/75/2284717//theVoid.2284717/1 -pa 1
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
flattening protein clusters
deleted:0 hits
collecting blastx reports
deleted:0 hits
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
preparing evidence clusters for annotations
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Preparing evidence for hint based annotation
running  blast search.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
processing chunk output
prepare section files
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/2/2284366.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/31/2284760.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
doing blastx of proteins
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
prepare section files
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:21   current j:0
 j_size:21   current j:1
 j_size:21   current j:2
 j_size:21   current j:3
 j_size:21   current j:4
 j_size:21   current j:5
 j_size:21   current j:6
 j_size:21   current j:7
 j_size:21   current j:8
 j_size:21   current j:9
 j_size:21   current j:10
 j_size:21   current j:11
 j_size:21   current j:12
 j_size:21   current j:13
 j_size:21   current j:14
 j_size:21   current j:15
 j_size:21   current j:16
 j_size:21   current j:17
 j_size:21   current j:18
 j_size:21   current j:19
 j_size:21   current j:20
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/29/2284809.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/41/2284722.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
prepare section files
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/10/2284707.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/0/2284707.9.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
flattening protein clusters
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0/2284801.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/93/33/2284801//theVoid.2284801/0 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
adding statistics to annotations
Calculating annotation quality statistics
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/1/2284688.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/1/2284688.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
choosing best annotation set
Choosing best annotations
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
deleted:0 hits
choosing best annotation set
Choosing best annotations
deleted:0 hits
deleted:0 hits
processing all repeats
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:14   current j:0
 j_size:14   current j:1
 j_size:14   current j:2
 j_size:14   current j:3
 j_size:14   current j:4
 j_size:14   current j:5
 j_size:14   current j:6
 j_size:14   current j:7
 j_size:14   current j:8
 j_size:14   current j:9
 j_size:14   current j:10
 j_size:14   current j:11
 j_size:14   current j:12
 j_size:14   current j:13
...finished clustering.
doing blastx repeats
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/24/2284752.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/20/2284776.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/41/2284722.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/32/2284825.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1/2284760.13.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/70/42/2284760//theVoid.2284760/1 -pa 1
#-------------------------------#
deleted:0 hits
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/7/2284347.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.28.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
preparing evidence clusters for annotations
running  blast search.
Preparing evidence for hint based annotation
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/30/2283486.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
prepare section files
 sorting hits in shadow cluster...
 j_size:11   current j:0
 j_size:11   current j:1
 j_size:11   current j:2
 j_size:11   current j:3
 j_size:11   current j:4
 j_size:11   current j:5
 j_size:11   current j:6
 j_size:11   current j:7
 j_size:11   current j:8
 j_size:11   current j:9
 j_size:11   current j:10
...finished clustering.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0/2284809.7.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D7/34/2284809//theVoid.2284809/0 -pa 1
#-------------------------------#
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/42/2284777.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/43/2284298.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.20.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/3/2284436.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.25.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/2/2284688.20.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/11/60/2284688//theVoid.2284688/2 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/8/2284700.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.5.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx repeatmasking
merging blast reports...
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/5/2284827.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
choosing best annotation set
Choosing best annotations
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/22/2284742.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
collecting blastx repeatmasking
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
collecting blastx reports
merging blast reports...
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
deleted:0 hits
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:24   current j:0
 j_size:24   current j:1
 j_size:24   current j:2
 j_size:24   current j:3
 j_size:24   current j:4
 j_size:24   current j:5
 j_size:24   current j:6
 j_size:24   current j:7
 j_size:24   current j:8
 j_size:24   current j:9
 j_size:24   current j:10
 j_size:24   current j:11
 j_size:24   current j:12
 j_size:24   current j:13
 j_size:24   current j:14
 j_size:24   current j:15
 j_size:24   current j:16
 j_size:24   current j:17
 j_size:24   current j:18
 j_size:24   current j:19
 j_size:24   current j:20
 j_size:24   current j:21
 j_size:24   current j:22
 j_size:24   current j:23
...finished clustering.
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
merging blast reports...
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
choosing best annotation set
Choosing best annotations
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
deleted:0 hits
deleted:0 hits
deleted:0 hits
flattening protein clusters
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
doing blastx of proteins
in cluster::shadow_cluster...
doing blastx of proteins
 sorting hits in shadow cluster...
 j_size:7   current j:0
 j_size:7   current j:1
 j_size:7   current j:2
 j_size:7   current j:3
 j_size:7   current j:4
 j_size:7   current j:5
 j_size:7   current j:6
...finished clustering.
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/41/2284722.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/33/2284220.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/23/2284552.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/17/2284642.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/3/sp%7CQ5ZJ56%7CRL7_CHICK.for.2528855-2533108.3.fasta -t /tmp/maker_6B3o0i/3/2284436.2528855-2533108.3.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/3/2284436.2528855-2533108.sp%7CQ5ZJ56%7CRL7_CHICK.p.exonerate
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/21/2284726.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/20/2284776.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing chunk output
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0/2284825.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/22/C0/2284825//theVoid.2284825/0 -pa 1
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
doing blastx of proteins
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1/2284752.14.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/C7/73/2284752//theVoid.2284752/1 -pa 1
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/14/2284530.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.17.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
flattening protein clusters
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/19/2284828.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
deleted:0 hits
deleted:1 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/21/2284726.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/13/2284676.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing blastx repeats
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/37/2284765.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:13   current j:0
 j_size:13   current j:1
 j_size:13   current j:2
 j_size:13   current j:3
 j_size:13   current j:4
 j_size:13   current j:5
 j_size:13   current j:6
 j_size:13   current j:7
 j_size:13   current j:8
 j_size:13   current j:9
 j_size:13   current j:10
 j_size:13   current j:11
 j_size:13   current j:12
...finished clustering.
deleted:0 hits
collecting blastx repeatmasking
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/27/2284424.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/33/2284220.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/41/2284722.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/17/0E/2284722//theVoid.2284722/1/2284722.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
deleted:0 hits
doing blastx of proteins
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/2/2284753.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/95/B8/2284753//theVoid.2284753/1/2284753.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/11/2284727.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.11.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
prepare section files
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
doing blastx of proteins
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
prepare section files
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
merging blast reports...
deleted:0 hits
doing blastx repeats
doing blastx repeats
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/20/2284776.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/23/2284552.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BC/51/2284552//theVoid.2284552/2/2284552.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
running  blast search.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/37/2284765.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx repeats
processing all repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/16/2284120.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/56/71/2284120//theVoid.2284120/4/2284120.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
in cluster::shadow_cluster...
doing blastx of proteins
running  blast search.
 sorting hits in shadow cluster...
 j_size:17   current j:0
 j_size:17   current j:1
 j_size:17   current j:2
 j_size:17   current j:3
 j_size:17   current j:4
 j_size:17   current j:5
 j_size:17   current j:6
 j_size:17   current j:7
 j_size:17   current j:8
 j_size:17   current j:9
 j_size:17   current j:10
 j_size:17   current j:11
 j_size:17   current j:12
 j_size:17   current j:13
 j_size:17   current j:14
 j_size:17   current j:15
 j_size:17   current j:16
...finished clustering.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/35/2284571.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/E8/AC/2284571//theVoid.2284571/1/2284571.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
clustering transcripts into genes for annotations
Processing transcripts into genes
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
collecting blastx reports
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1/2284742.15.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/77/26/2284742//theVoid.2284742/1 -pa 1
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/28/2284616.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/F3/B2/2284616//theVoid.2284616/1/2284616.14.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
doing blastx of proteins
running  blast search.
doing blastx repeats
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/33/2284220.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:10   current j:0
 j_size:10   current j:1
 j_size:10   current j:2
 j_size:10   current j:3
 j_size:10   current j:4
 j_size:10   current j:5
 j_size:10   current j:6
 j_size:10   current j:7
 j_size:10   current j:8
 j_size:10   current j:9
...finished clustering.
merging blast reports...
clustering transcripts into genes for annotations
Processing transcripts into genes
doing blastx of proteins
collecting blastx reports
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/9/2284744.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/C8/2284744//theVoid.2284744/1/2284744.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/20/2284776.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/21/2284726.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/1F/9D/2284726//theVoid.2284726/1/2284726.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/26/2284607.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/2F/47/2284607//theVoid.2284607/0/2284607.2.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/12/2284673.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/15/33/2284673//theVoid.2284673/2/2284673.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
flattening protein clusters
doing repeat masking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
flattening protein clusters
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1/2284777.12.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4D/4F/2284777//theVoid.2284777/1 -pa 1
#-------------------------------#
doing repeat masking
collecting blastx reports
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0/2284827.5.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/91/BE/2284827//theVoid.2284827/0 -pa 1
#-------------------------------#
flattening protein clusters
adding statistics to annotations
Calculating annotation quality statistics
processing all repeats
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:12   current j:0
 j_size:12   current j:1
 j_size:12   current j:2
 j_size:12   current j:3
 j_size:12   current j:4
 j_size:12   current j:5
 j_size:12   current j:6
 j_size:12   current j:7
 j_size:12   current j:8
 j_size:12   current j:9
 j_size:12   current j:10
 j_size:12   current j:11
...finished clustering.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
merging blast reports...
merging blast reports...
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.6 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.6.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/17/2284642.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/B7/A9/2284642//theVoid.2284642/2/2284642.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
prepare section files
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/15/2284788.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
deleted:0 hits
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/18/2284366.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/D4/88/2284366//theVoid.2284366/3/2284366.30.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
doing blastx of proteins
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
prepare section files
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing repeat masking
flattening protein clusters
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_6B3o0i; /group/bioinfo/apps/apps/RepeatMasker-4.0.3/RepeatMasker /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0/2284828.2.all.rb -species all -dir /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/4E/65/2284828//theVoid.2284828/0 -pa 1
#-------------------------------#
prepare section files
flattening protein clusters
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
choosing best annotation set
Choosing best annotations
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
deleted:1 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
collecting blastx repeatmasking
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.7 -query /tmp/maker_6B3o0i/10/2284707.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/5F/6F/2284707//theVoid.2284707/1/2284707.10.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.7.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx repeatmasking
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.9 -query /tmp/maker_6B3o0i/4/2283926.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/16/23/2283926//theVoid.2283926/1/2283926.19.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.9.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/30/2283486.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/90/EF/2283486//theVoid.2283486/0/2283486.7.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/33/2284220.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BD/CC/2284220//theVoid.2284220/4/2284220.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
collecting blastx reports
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/11/2284727.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0D/91/2284727//theVoid.2284727/1/2284727.12.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
prepare section files
prepare section files
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
merging blast reports...
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/40/2284824.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/28/90/2284824//theVoid.2284824/0/2284824.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/37/2284765.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/BA/7D/2284765//theVoid.2284765/1/2284765.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
processing chunk output
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.0 -query /tmp/maker_6B3o0i/27/2284424.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/12/04/2284424//theVoid.2284424/2/2284424.22.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.0.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.5 -query /tmp/maker_6B3o0i/7/2284347.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/6C/50/2284347//theVoid.2284347/2/2284347.29.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.5.blastx
#-------------------------------#
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_6B3o0i/6/2284509.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/05/59/2284509//theVoid.2284509/3/2284509.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.2 -query /tmp/maker_6B3o0i/8/2284700.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/AC/A1/2284700//theVoid.2284700/0/2284700.6.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
Use of uninitialized value $from in string eq at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 102.
Use of uninitialized value $from in stat at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 138.
Use of uninitialized value $from in open at /apps/group/bioinformatics/apps/perl-5.16.1/lib/5.16.1/File/Copy.pm line 215.
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.3 -query /tmp/maker_6B3o0i/3/2284436.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/EB/7F/2284436//theVoid.2284436/2/2284436.26.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.3.blastx
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/14/2284530.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/0C/04/2284530//theVoid.2284530/1/2284530.18.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/15/2284788.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/41/B8/2284788//theVoid.2284788/0/2284788.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/43/2284298.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/09/78/2284298//theVoid.2284298/2/2284298.21.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.4.blastx
#-------------------------------#
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_6B3o0i/20/2284776.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/A0/F0/2284776//theVoid.2284776/1/2284776.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
polishing proteins
doing blastx repeats
doing blastx of proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/group/bioinfo/apps/apps/exonerate-2.2.0/bin/exonerate -q /tmp/maker_6B3o0i/18/sp%7CO57337%7CHES1_CHICK.for.3014234-3015564.18.fasta -t /tmp/maker_6B3o0i/18/2284366.3014234-3015564.18.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_6B3o0i/18/2284366.3014234-3015564.sp%7CO57337%7CHES1_CHICK.p.exonerate
#-------------------------------#
running  blast search.
running  blast search.
#--------- command -------------#
Widget::blastx:
/apps/group/bioinformatics/apps/blast-2.2.28+/bin/blastx -db /tmp/maker_6B3o0i/avianuniprot%2Efasta.mpi.10.1 -query /tmp/maker_6B3o0i/13/2284676.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /scratch/lustreC/j/jmdoyle/kmer70_min1200000_scaffolds_revisedassembly.maker.output/kmer70_min1200000_scaffolds_revisedassembly_datastore/7A/05/2284676//theVoid.2284676/1/2284676.13.avianuniprot%2Efasta.blastx.temp_dir/avianuniprot%2Efasta.mpi.10.1.blastx
#-------------------------------#
#--------- command -------------#
Wi